I-H-108333

Patient I-H-108333

View Patient in Leukgen

Individual DMP ID: P-0006237

Gender: MALE

Disease(s): UNDIFFERENTIATED SARCOMA (UNDIFS)

Part C Consent: True

Number of WGS Samples: 1

Number of RNAseq Samples: 1

CBio Portal Results:

Tumor_Sample_Barcode Chromosome Start_Position Reference_Allele Tumor_Seq_Allele2 Hugo_Symbol VAF Variant_Classification HGVSp_Short
P-0006237-T04-IM6 3 178917478 G A PIK3CA 0.270423 Missense_Mutation p.G118D 

          

        

        

          

          

            
RNA Sample: I-H-108333-T2-1-R1-1
            

          

        

        

          

          

            
Disease: UNDIFFERENTIATED SARCOMA (UNDIFS)

          

        

        

          

          

            
Tissue Site: R Gluteal Mass

          

        

        

          

          

            
Days since birth at collection: 8029

          

        

        

          

          

            

          

        

        

          

          

            
Fusion Results:

            

          

        

        

          

          

            
High Confidence Fusions:

          

        

        

          

          

            
            

              
              
                  
                    
                    
                    
                    
                    
                    
                    
                    
                    
                    
                    
                  
                

                
                  

                    GENE1
                    GENE2
                    DESCRIPTION
                    SPAN_READS
                    SPLIT_READS
                    LEFTBREAK
                    RIGHTBREAK
                    CALLER_EFFECT
                    ANNOT_EFFECT
                    CALLER
                    NUM_CALLERS
                  

                
                
                  
                  
                  
                  
                  
                  
                  
                  
                  
                  
                  
                

                
                  

                    MGA
                    NUTM1
                    
                      oncogene,cancer,exon-exon
                    14
                    19
                    15:42054560:+
                    15:34640170:+
                    in-frame
                    in-frame
                    FUSIONCATCHER
                    3
                  

                
                
              

            

          

        

        

          

          

            

            
          

        

        

          

          

            
View RNAFUSIONS Report

          

        

        

          

          

            

          

        

        

          

          

            
Expression TSNE
              Results:

            

          

        

        

          

          





            
            Bokeh Application
            
            
            


            

              

                

                  

                    

                      
                    

                    

                      

                        

                          

                            

                          

                          

                            

                            

                          

                          

                            

                          

                        

                      

                    

                  

                

              

            

          

        

        

          

          

            

          

        

        

          

          

            
Overexpressed Cancer
              Genes:

            

          

        

        

          

          

            
            

              
              
                  
                    
                    
                    
                    
                  
                

                
                  

                    Gene
                    Log Fold Change
                    Loc
                    Cancers
                  

                
                
                  
                  
                  
                  
                

                
                  

                    NUTM1
                    7.61806
                    15q14
                    lethal midline
                      carcinoma
                  

                  

                    OLIG2
                    4.29052
                    21q22.11
                    T-ALL
                  

                  

                    MLF1
                    3.65278
                    3q25.1
                    AML
                  

                  

                    LRIG3
                    2.29114
                    12q14.1
                    NSCLC
                  

                  

                    SFRP4
                    2.16084
                    7p14.1
                    colorectal cancer,
                      melanoma, SCC, gastric cancer, oesophageal SCC
                  

                
                
              

            

          

        

        

          

          

            

          

        

        

          

          

            
WGS Sample: I-H-108333-T2-2-D1-1
            

          

        

        

          

          

            
Disease: UNDIFFERENTIATED SARCOMA (UNDIFS)

          

        

        

          

          

            
Tissue Site: R Gluteal Mass

          

        

        

          

          

            
Days since birth at collection: 8029

          

        

        

          

          

            
Normal used: I-H-108333-N2-1-D1-1
            

          

        

        

          

          

            
Median Coverage: 115

          

        

        

          

          

            
MSISensor HAS NOT BEEN RUN

          

        

        

          

          

            

          

        

        

          

          

            
Copy Number Results:

            

          

        

        

          

          

            
Tumor Purity: 0.9

          

        

        

          

          

            
Tumor Ploidy: 2.24
            

          

        

        

          


        

        

          

          

            
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
              src="data:image/svg+xml;base64,<?xml version="1.0" encoding="utf-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Created with matplotlib (http://matplotlib.org/) -->
<svg height="318.947403pt" version="1.1" viewBox="0 0 694.024409 318.947403" width="694.024409pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
 <defs>
  <style type="text/css">
*{stroke-linecap:butt;stroke-linejoin:round;}
  </style>
 </defs>
 <g id="figure_1">
  <g id="patch_1">
   <path d="M 0 318.947403 
L 694.024409 318.947403 
L 694.024409 0 
L 0 0 
z
" style="fill:#ffffff;"/>
  </g>
  <g id="axes_1">
   <g id="patch_2">
    <path d="M 110.602284 279 
L 629.542284 279 
L 629.542284 7.2 
L 110.602284 7.2 
z
" style="fill:#dddddd;"/>
   </g>
   <g id="matplotlib.axis_1">
    <g id="xtick_1">
     <g id="line2d_1"/>
     <g id="text_1">
      <!-- 1 -->
      <defs>
       <path d="M 12.40625 8.296875 
L 28.515625 8.296875 
L 28.515625 63.921875 
L 10.984375 60.40625 
L 10.984375 69.390625 
L 28.421875 72.90625 
L 38.28125 72.90625 
L 38.28125 8.296875 
L 54.390625 8.296875 
L 54.390625 0 
L 12.40625 0 
z
" id="DejaVuSans-31"/>
      </defs>
      <g style="fill:#262626;" transform="translate(132.061388 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_2">
     <g id="line2d_2"/>
     <g id="text_2">
      <!-- 2 -->
      <defs>
       <path d="M 19.1875 8.296875 
L 53.609375 8.296875 
L 53.609375 0 
L 7.328125 0 
L 7.328125 8.296875 
Q 12.9375 14.109375 22.625 23.890625 
Q 32.328125 33.6875 34.8125 36.53125 
Q 39.546875 41.84375 41.421875 45.53125 
Q 43.3125 49.21875 43.3125 52.78125 
Q 43.3125 58.59375 39.234375 62.25 
Q 35.15625 65.921875 28.609375 65.921875 
Q 23.96875 65.921875 18.8125 64.3125 
Q 13.671875 62.703125 7.8125 59.421875 
L 7.8125 69.390625 
Q 13.765625 71.78125 18.9375 73 
Q 24.125 74.21875 28.421875 74.21875 
Q 39.75 74.21875 46.484375 68.546875 
Q 53.21875 62.890625 53.21875 53.421875 
Q 53.21875 48.921875 51.53125 44.890625 
Q 49.859375 40.875 45.40625 35.40625 
Q 44.1875 33.984375 37.640625 27.21875 
Q 31.109375 20.453125 19.1875 8.296875 
z
" id="DejaVuSans-32"/>
      </defs>
      <g style="fill:#262626;" transform="translate(173.353465 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_3">
     <g id="line2d_3"/>
     <g id="text_3">
      <!-- 3 -->
      <defs>
       <path d="M 40.578125 39.3125 
Q 47.65625 37.796875 51.625 33 
Q 55.609375 28.21875 55.609375 21.1875 
Q 55.609375 10.40625 48.1875 4.484375 
Q 40.765625 -1.421875 27.09375 -1.421875 
Q 22.515625 -1.421875 17.65625 -0.515625 
Q 12.796875 0.390625 7.625 2.203125 
L 7.625 11.71875 
Q 11.71875 9.328125 16.59375 8.109375 
Q 21.484375 6.890625 26.8125 6.890625 
Q 36.078125 6.890625 40.9375 10.546875 
Q 45.796875 14.203125 45.796875 21.1875 
Q 45.796875 27.640625 41.28125 31.265625 
Q 36.765625 34.90625 28.71875 34.90625 
L 20.21875 34.90625 
L 20.21875 43.015625 
L 29.109375 43.015625 
Q 36.375 43.015625 40.234375 45.921875 
Q 44.09375 48.828125 44.09375 54.296875 
Q 44.09375 59.90625 40.109375 62.90625 
Q 36.140625 65.921875 28.71875 65.921875 
Q 24.65625 65.921875 20.015625 65.03125 
Q 15.375 64.15625 9.8125 62.3125 
L 9.8125 71.09375 
Q 15.4375 72.65625 20.34375 73.4375 
Q 25.25 74.21875 29.59375 74.21875 
Q 40.828125 74.21875 47.359375 69.109375 
Q 53.90625 64.015625 53.90625 55.328125 
Q 53.90625 49.265625 50.4375 45.09375 
Q 46.96875 40.921875 40.578125 39.3125 
z
" id="DejaVuSans-33"/>
      </defs>
      <g style="fill:#262626;" transform="translate(210.344236 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_4">
     <g id="line2d_4"/>
     <g id="text_4">
      <!-- 4 -->
      <defs>
       <path d="M 37.796875 64.3125 
L 12.890625 25.390625 
L 37.796875 25.390625 
z
M 35.203125 72.90625 
L 47.609375 72.90625 
L 47.609375 25.390625 
L 58.015625 25.390625 
L 58.015625 17.1875 
L 47.609375 17.1875 
L 47.609375 0 
L 37.796875 0 
L 37.796875 17.1875 
L 4.890625 17.1875 
L 4.890625 26.703125 
z
" id="DejaVuSans-34"/>
      </defs>
      <g style="fill:#262626;" transform="translate(242.958486 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_5">
     <g id="line2d_5"/>
     <g id="text_5">
      <!-- 5 -->
      <defs>
       <path d="M 10.796875 72.90625 
L 49.515625 72.90625 
L 49.515625 64.59375 
L 19.828125 64.59375 
L 19.828125 46.734375 
Q 21.96875 47.46875 24.109375 47.828125 
Q 26.265625 48.1875 28.421875 48.1875 
Q 40.625 48.1875 47.75 41.5 
Q 54.890625 34.8125 54.890625 23.390625 
Q 54.890625 11.625 47.5625 5.09375 
Q 40.234375 -1.421875 26.90625 -1.421875 
Q 22.3125 -1.421875 17.546875 -0.640625 
Q 12.796875 0.140625 7.71875 1.703125 
L 7.71875 11.625 
Q 12.109375 9.234375 16.796875 8.0625 
Q 21.484375 6.890625 26.703125 6.890625 
Q 35.15625 6.890625 40.078125 11.328125 
Q 45.015625 15.765625 45.015625 23.390625 
Q 45.015625 31 40.078125 35.4375 
Q 35.15625 39.890625 26.703125 39.890625 
Q 22.75 39.890625 18.8125 39.015625 
Q 14.890625 38.140625 10.796875 36.28125 
z
" id="DejaVuSans-35"/>
      </defs>
      <g style="fill:#262626;" transform="translate(274.143844 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_6">
     <g id="line2d_6"/>
     <g id="text_6">
      <!-- 6 -->
      <defs>
       <path d="M 33.015625 40.375 
Q 26.375 40.375 22.484375 35.828125 
Q 18.609375 31.296875 18.609375 23.390625 
Q 18.609375 15.53125 22.484375 10.953125 
Q 26.375 6.390625 33.015625 6.390625 
Q 39.65625 6.390625 43.53125 10.953125 
Q 47.40625 15.53125 47.40625 23.390625 
Q 47.40625 31.296875 43.53125 35.828125 
Q 39.65625 40.375 33.015625 40.375 
z
M 52.59375 71.296875 
L 52.59375 62.3125 
Q 48.875 64.0625 45.09375 64.984375 
Q 41.3125 65.921875 37.59375 65.921875 
Q 27.828125 65.921875 22.671875 59.328125 
Q 17.53125 52.734375 16.796875 39.40625 
Q 19.671875 43.65625 24.015625 45.921875 
Q 28.375 48.1875 33.59375 48.1875 
Q 44.578125 48.1875 50.953125 41.515625 
Q 57.328125 34.859375 57.328125 23.390625 
Q 57.328125 12.15625 50.6875 5.359375 
Q 44.046875 -1.421875 33.015625 -1.421875 
Q 20.359375 -1.421875 13.671875 8.265625 
Q 6.984375 17.96875 6.984375 36.375 
Q 6.984375 53.65625 15.1875 63.9375 
Q 23.390625 74.21875 37.203125 74.21875 
Q 40.921875 74.21875 44.703125 73.484375 
Q 48.484375 72.75 52.59375 71.296875 
z
" id="DejaVuSans-36"/>
      </defs>
      <g style="fill:#262626;" transform="translate(303.653886 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_7">
     <g id="line2d_7"/>
     <g id="text_7">
      <!-- 7 -->
      <defs>
       <path d="M 8.203125 72.90625 
L 55.078125 72.90625 
L 55.078125 68.703125 
L 28.609375 0 
L 18.3125 0 
L 43.21875 64.59375 
L 8.203125 64.59375 
z
" id="DejaVuSans-37"/>
      </defs>
      <g style="fill:#262626;" transform="translate(331.337885 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_8">
     <g id="line2d_8"/>
     <g id="text_8">
      <!-- 8 -->
      <defs>
       <path d="M 31.78125 34.625 
Q 24.75 34.625 20.71875 30.859375 
Q 16.703125 27.09375 16.703125 20.515625 
Q 16.703125 13.921875 20.71875 10.15625 
Q 24.75 6.390625 31.78125 6.390625 
Q 38.8125 6.390625 42.859375 10.171875 
Q 46.921875 13.96875 46.921875 20.515625 
Q 46.921875 27.09375 42.890625 30.859375 
Q 38.875 34.625 31.78125 34.625 
z
M 21.921875 38.8125 
Q 15.578125 40.375 12.03125 44.71875 
Q 8.5 49.078125 8.5 55.328125 
Q 8.5 64.0625 14.71875 69.140625 
Q 20.953125 74.21875 31.78125 74.21875 
Q 42.671875 74.21875 48.875 69.140625 
Q 55.078125 64.0625 55.078125 55.328125 
Q 55.078125 49.078125 51.53125 44.71875 
Q 48 40.375 41.703125 38.8125 
Q 48.828125 37.15625 52.796875 32.3125 
Q 56.78125 27.484375 56.78125 20.515625 
Q 56.78125 9.90625 50.3125 4.234375 
Q 43.84375 -1.421875 31.78125 -1.421875 
Q 19.734375 -1.421875 13.25 4.234375 
Q 6.78125 9.90625 6.78125 20.515625 
Q 6.78125 27.484375 10.78125 32.3125 
Q 14.796875 37.15625 21.921875 38.8125 
z
M 18.3125 54.390625 
Q 18.3125 48.734375 21.84375 45.5625 
Q 25.390625 42.390625 31.78125 42.390625 
Q 38.140625 42.390625 41.71875 45.5625 
Q 45.3125 48.734375 45.3125 54.390625 
Q 45.3125 60.0625 41.71875 63.234375 
Q 38.140625 66.40625 31.78125 66.40625 
Q 25.390625 66.40625 21.84375 63.234375 
Q 18.3125 60.0625 18.3125 54.390625 
z
" id="DejaVuSans-38"/>
      </defs>
      <g style="fill:#262626;" transform="translate(356.949539 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_9">
     <g id="line2d_9"/>
     <g id="text_9">
      <!-- 9 -->
      <defs>
       <path d="M 10.984375 1.515625 
L 10.984375 10.5 
Q 14.703125 8.734375 18.5 7.8125 
Q 22.3125 6.890625 25.984375 6.890625 
Q 35.75 6.890625 40.890625 13.453125 
Q 46.046875 20.015625 46.78125 33.40625 
Q 43.953125 29.203125 39.59375 26.953125 
Q 35.25 24.703125 29.984375 24.703125 
Q 19.046875 24.703125 12.671875 31.3125 
Q 6.296875 37.9375 6.296875 49.421875 
Q 6.296875 60.640625 12.9375 67.421875 
Q 19.578125 74.21875 30.609375 74.21875 
Q 43.265625 74.21875 49.921875 64.515625 
Q 56.59375 54.828125 56.59375 36.375 
Q 56.59375 19.140625 48.40625 8.859375 
Q 40.234375 -1.421875 26.421875 -1.421875 
Q 22.703125 -1.421875 18.890625 -0.6875 
Q 15.09375 0.046875 10.984375 1.515625 
z
M 30.609375 32.421875 
Q 37.25 32.421875 41.125 36.953125 
Q 45.015625 41.5 45.015625 49.421875 
Q 45.015625 57.28125 41.125 61.84375 
Q 37.25 66.40625 30.609375 66.40625 
Q 23.96875 66.40625 20.09375 61.84375 
Q 16.21875 57.28125 16.21875 49.421875 
Q 16.21875 41.5 20.09375 36.953125 
Q 23.96875 32.421875 30.609375 32.421875 
z
" id="DejaVuSans-39"/>
      </defs>
      <g style="fill:#262626;" transform="translate(381.053879 292.516514)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_10">
     <g id="line2d_10"/>
     <g id="text_10">
      <!-- 10 -->
      <defs>
       <path d="M 31.78125 66.40625 
Q 24.171875 66.40625 20.328125 58.90625 
Q 16.5 51.421875 16.5 36.375 
Q 16.5 21.390625 20.328125 13.890625 
Q 24.171875 6.390625 31.78125 6.390625 
Q 39.453125 6.390625 43.28125 13.890625 
Q 47.125 21.390625 47.125 36.375 
Q 47.125 51.421875 43.28125 58.90625 
Q 39.453125 66.40625 31.78125 66.40625 
z
M 31.78125 74.21875 
Q 44.046875 74.21875 50.515625 64.515625 
Q 56.984375 54.828125 56.984375 36.375 
Q 56.984375 17.96875 50.515625 8.265625 
Q 44.046875 -1.421875 31.78125 -1.421875 
Q 19.53125 -1.421875 13.0625 8.265625 
Q 6.59375 17.96875 6.59375 36.375 
Q 6.59375 54.828125 13.0625 64.515625 
Q 19.53125 74.21875 31.78125 74.21875 
z
" id="DejaVuSans-30"/>
      </defs>
      <g style="fill:#262626;" transform="translate(403.137881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_11">
     <g id="line2d_11"/>
     <g id="text_11">
      <!-- 11 -->
      <g style="fill:#262626;" transform="translate(425.814881 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_12">
     <g id="line2d_12"/>
     <g id="text_12">
      <!-- 12 -->
      <g style="fill:#262626;" transform="translate(448.353061 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_13">
     <g id="line2d_13"/>
     <g id="text_13">
      <!-- 13 -->
      <g style="fill:#262626;" transform="translate(469.227832 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-33"/>
      </g>
     </g>
    </g>
    <g id="xtick_14">
     <g id="line2d_14"/>
     <g id="text_14">
      <!-- 14 -->
      <g style="fill:#262626;" transform="translate(487.876806 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-34"/>
      </g>
     </g>
    </g>
    <g id="xtick_15">
     <g id="line2d_15"/>
     <g id="text_15">
      <!-- 15 -->
      <g style="fill:#262626;" transform="translate(505.470187 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="xtick_16">
     <g id="line2d_16"/>
     <g id="text_16">
      <!-- 16 -->
      <g style="fill:#262626;" transform="translate(521.63847 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="xtick_17">
     <g id="line2d_17"/>
     <g id="text_17">
      <!-- 17 -->
      <g style="fill:#262626;" transform="translate(536.018517 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-37"/>
      </g>
     </g>
    </g>
    <g id="xtick_18">
     <g id="line2d_18"/>
     <g id="text_18">
      <!-- 18 -->
      <g style="fill:#262626;" transform="translate(549.369047 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-38"/>
      </g>
     </g>
    </g>
    <g id="xtick_19">
     <g id="line2d_19"/>
     <g id="text_19">
      <!-- 19 -->
      <g style="fill:#262626;" transform="translate(560.868347 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-31"/>
       <use x="63.623047" xlink:href="#DejaVuSans-39"/>
      </g>
     </g>
    </g>
    <g id="xtick_20">
     <g id="line2d_20"/>
     <g id="text_20">
      <!-- 20 -->
      <g style="fill:#262626;" transform="translate(571.105521 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="xtick_21">
     <g id="line2d_21"/>
     <g id="text_21">
      <!-- 21 -->
      <g style="fill:#262626;" transform="translate(580.420386 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="xtick_22">
     <g id="line2d_22"/>
     <g id="text_22">
      <!-- 22 -->
      <g style="fill:#262626;" transform="translate(588.752401 296.373574)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-32"/>
       <use x="63.623047" xlink:href="#DejaVuSans-32"/>
      </g>
     </g>
    </g>
    <g id="xtick_23">
     <g id="line2d_23"/>
     <g id="text_23">
      <!-- X -->
      <defs>
       <path d="M 6.296875 72.90625 
L 16.890625 72.90625 
L 35.015625 45.796875 
L 53.21875 72.90625 
L 63.8125 72.90625 
L 40.375 37.890625 
L 65.375 0 
L 54.78125 0 
L 34.28125 31 
L 13.625 0 
L 2.984375 0 
L 29 38.921875 
z
" id="DejaVuSans-58"/>
      </defs>
      <g style="fill:#262626;" transform="translate(607.096727 292.812045)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-58"/>
      </g>
     </g>
    </g>
    <g id="xtick_24">
     <g id="line2d_24"/>
     <g id="text_24">
      <!-- Y -->
      <defs>
       <path d="M -0.203125 72.90625 
L 10.40625 72.90625 
L 30.609375 42.921875 
L 50.6875 72.90625 
L 61.28125 72.90625 
L 35.5 34.71875 
L 35.5 0 
L 25.59375 0 
L 25.59375 34.71875 
z
" id="DejaVuSans-59"/>
      </defs>
      <g style="fill:#262626;" transform="translate(625.195991 292.362118)rotate(-60)scale(0.07 -0.07)">
       <use xlink:href="#DejaVuSans-59"/>
      </g>
     </g>
    </g>
    <g id="text_25">
     <!-- Chromosome -->
     <defs>
      <path d="M 64.40625 67.28125 
L 64.40625 56.890625 
Q 59.421875 61.53125 53.78125 63.8125 
Q 48.140625 66.109375 41.796875 66.109375 
Q 29.296875 66.109375 22.65625 58.46875 
Q 16.015625 50.828125 16.015625 36.375 
Q 16.015625 21.96875 22.65625 14.328125 
Q 29.296875 6.6875 41.796875 6.6875 
Q 48.140625 6.6875 53.78125 8.984375 
Q 59.421875 11.28125 64.40625 15.921875 
L 64.40625 5.609375 
Q 59.234375 2.09375 53.4375 0.328125 
Q 47.65625 -1.421875 41.21875 -1.421875 
Q 24.65625 -1.421875 15.125 8.703125 
Q 5.609375 18.84375 5.609375 36.375 
Q 5.609375 53.953125 15.125 64.078125 
Q 24.65625 74.21875 41.21875 74.21875 
Q 47.75 74.21875 53.53125 72.484375 
Q 59.328125 70.75 64.40625 67.28125 
z
" id="DejaVuSans-43"/>
      <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-68"/>
      <path d="M 41.109375 46.296875 
Q 39.59375 47.171875 37.8125 47.578125 
Q 36.03125 48 33.890625 48 
Q 26.265625 48 22.1875 43.046875 
Q 18.109375 38.09375 18.109375 28.8125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 20.953125 51.171875 25.484375 53.578125 
Q 30.03125 56 36.53125 56 
Q 37.453125 56 38.578125 55.875 
Q 39.703125 55.765625 41.0625 55.515625 
z
" id="DejaVuSans-72"/>
      <path d="M 30.609375 48.390625 
Q 23.390625 48.390625 19.1875 42.75 
Q 14.984375 37.109375 14.984375 27.296875 
Q 14.984375 17.484375 19.15625 11.84375 
Q 23.34375 6.203125 30.609375 6.203125 
Q 37.796875 6.203125 41.984375 11.859375 
Q 46.1875 17.53125 46.1875 27.296875 
Q 46.1875 37.015625 41.984375 42.703125 
Q 37.796875 48.390625 30.609375 48.390625 
z
M 30.609375 56 
Q 42.328125 56 49.015625 48.375 
Q 55.71875 40.765625 55.71875 27.296875 
Q 55.71875 13.875 49.015625 6.21875 
Q 42.328125 -1.421875 30.609375 -1.421875 
Q 18.84375 -1.421875 12.171875 6.21875 
Q 5.515625 13.875 5.515625 27.296875 
Q 5.515625 40.765625 12.171875 48.375 
Q 18.84375 56 30.609375 56 
z
" id="DejaVuSans-6f"/>
      <path d="M 52 44.1875 
Q 55.375 50.25 60.0625 53.125 
Q 64.75 56 71.09375 56 
Q 79.640625 56 84.28125 50.015625 
Q 88.921875 44.046875 88.921875 33.015625 
L 88.921875 0 
L 79.890625 0 
L 79.890625 32.71875 
Q 79.890625 40.578125 77.09375 44.375 
Q 74.3125 48.1875 68.609375 48.1875 
Q 61.625 48.1875 57.5625 43.546875 
Q 53.515625 38.921875 53.515625 30.90625 
L 53.515625 0 
L 44.484375 0 
L 44.484375 32.71875 
Q 44.484375 40.625 41.703125 44.40625 
Q 38.921875 48.1875 33.109375 48.1875 
Q 26.21875 48.1875 22.15625 43.53125 
Q 18.109375 38.875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.1875 51.21875 25.484375 53.609375 
Q 29.78125 56 35.6875 56 
Q 41.65625 56 45.828125 52.96875 
Q 50 49.953125 52 44.1875 
z
" id="DejaVuSans-6d"/>
      <path d="M 44.28125 53.078125 
L 44.28125 44.578125 
Q 40.484375 46.53125 36.375 47.5 
Q 32.28125 48.484375 27.875 48.484375 
Q 21.1875 48.484375 17.84375 46.4375 
Q 14.5 44.390625 14.5 40.28125 
Q 14.5 37.15625 16.890625 35.375 
Q 19.28125 33.59375 26.515625 31.984375 
L 29.59375 31.296875 
Q 39.15625 29.25 43.1875 25.515625 
Q 47.21875 21.78125 47.21875 15.09375 
Q 47.21875 7.46875 41.1875 3.015625 
Q 35.15625 -1.421875 24.609375 -1.421875 
Q 20.21875 -1.421875 15.453125 -0.5625 
Q 10.6875 0.296875 5.421875 2 
L 5.421875 11.28125 
Q 10.40625 8.6875 15.234375 7.390625 
Q 20.0625 6.109375 24.8125 6.109375 
Q 31.15625 6.109375 34.5625 8.28125 
Q 37.984375 10.453125 37.984375 14.40625 
Q 37.984375 18.0625 35.515625 20.015625 
Q 33.0625 21.96875 24.703125 23.78125 
L 21.578125 24.515625 
Q 13.234375 26.265625 9.515625 29.90625 
Q 5.8125 33.546875 5.8125 39.890625 
Q 5.8125 47.609375 11.28125 51.796875 
Q 16.75 56 26.8125 56 
Q 31.78125 56 36.171875 55.265625 
Q 40.578125 54.546875 44.28125 53.078125 
z
" id="DejaVuSans-73"/>
      <path d="M 56.203125 29.59375 
L 56.203125 25.203125 
L 14.890625 25.203125 
Q 15.484375 15.921875 20.484375 11.0625 
Q 25.484375 6.203125 34.421875 6.203125 
Q 39.59375 6.203125 44.453125 7.46875 
Q 49.3125 8.734375 54.109375 11.28125 
L 54.109375 2.78125 
Q 49.265625 0.734375 44.1875 -0.34375 
Q 39.109375 -1.421875 33.890625 -1.421875 
Q 20.796875 -1.421875 13.15625 6.1875 
Q 5.515625 13.8125 5.515625 26.8125 
Q 5.515625 40.234375 12.765625 48.109375 
Q 20.015625 56 32.328125 56 
Q 43.359375 56 49.78125 48.890625 
Q 56.203125 41.796875 56.203125 29.59375 
z
M 47.21875 32.234375 
Q 47.125 39.59375 43.09375 43.984375 
Q 39.0625 48.390625 32.421875 48.390625 
Q 24.90625 48.390625 20.390625 44.140625 
Q 15.875 39.890625 15.1875 32.171875 
z
" id="DejaVuSans-65"/>
     </defs>
     <g style="fill:#262626;" transform="translate(333.426816 309.459746)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-43"/>
      <use x="69.824219" xlink:href="#DejaVuSans-68"/>
      <use x="133.203125" xlink:href="#DejaVuSans-72"/>
      <use x="174.285156" xlink:href="#DejaVuSans-6f"/>
      <use x="235.466797" xlink:href="#DejaVuSans-6d"/>
      <use x="332.878906" xlink:href="#DejaVuSans-6f"/>
      <use x="394.060547" xlink:href="#DejaVuSans-73"/>
      <use x="446.160156" xlink:href="#DejaVuSans-6f"/>
      <use x="507.341797" xlink:href="#DejaVuSans-6d"/>
      <use x="604.753906" xlink:href="#DejaVuSans-65"/>
     </g>
    </g>
   </g>
   <g id="matplotlib.axis_2">
    <g id="ytick_1">
     <g id="line2d_25"/>
     <g id="text_26">
      <!-- P-0006237-T01-IM5 -->
      <defs>
       <path d="M 19.671875 64.796875 
L 19.671875 37.40625 
L 32.078125 37.40625 
Q 38.96875 37.40625 42.71875 40.96875 
Q 46.484375 44.53125 46.484375 51.125 
Q 46.484375 57.671875 42.71875 61.234375 
Q 38.96875 64.796875 32.078125 64.796875 
z
M 9.8125 72.90625 
L 32.078125 72.90625 
Q 44.34375 72.90625 50.609375 67.359375 
Q 56.890625 61.8125 56.890625 51.125 
Q 56.890625 40.328125 50.609375 34.8125 
Q 44.34375 29.296875 32.078125 29.296875 
L 19.671875 29.296875 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-50"/>
       <path d="M 4.890625 31.390625 
L 31.203125 31.390625 
L 31.203125 23.390625 
L 4.890625 23.390625 
z
" id="DejaVuSans-2d"/>
       <path d="M -0.296875 72.90625 
L 61.375 72.90625 
L 61.375 64.59375 
L 35.5 64.59375 
L 35.5 0 
L 25.59375 0 
L 25.59375 64.59375 
L -0.296875 64.59375 
z
" id="DejaVuSans-54"/>
       <path d="M 9.8125 72.90625 
L 19.671875 72.90625 
L 19.671875 0 
L 9.8125 0 
z
" id="DejaVuSans-49"/>
       <path d="M 9.8125 72.90625 
L 24.515625 72.90625 
L 43.109375 23.296875 
L 61.8125 72.90625 
L 76.515625 72.90625 
L 76.515625 0 
L 66.890625 0 
L 66.890625 64.015625 
L 48.09375 14.015625 
L 38.1875 14.015625 
L 19.390625 64.015625 
L 19.390625 0 
L 9.8125 0 
z
" id="DejaVuSans-4d"/>
      </defs>
      <g style="fill:#262626;" transform="translate(21.845938 37.544749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-31"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-35"/>
      </g>
     </g>
    </g>
    <g id="ytick_2">
     <g id="line2d_26"/>
     <g id="text_27">
      <!-- P-0006237-T04-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 91.904749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-34"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_3">
     <g id="line2d_27"/>
     <g id="text_28">
      <!-- P-0006237-T05-IM6 -->
      <g style="fill:#262626;" transform="translate(21.845938 146.264749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-50"/>
       <use x="60.271484" xlink:href="#DejaVuSans-2d"/>
       <use x="96.355469" xlink:href="#DejaVuSans-30"/>
       <use x="159.978516" xlink:href="#DejaVuSans-30"/>
       <use x="223.601562" xlink:href="#DejaVuSans-30"/>
       <use x="287.224609" xlink:href="#DejaVuSans-36"/>
       <use x="350.847656" xlink:href="#DejaVuSans-32"/>
       <use x="414.470703" xlink:href="#DejaVuSans-33"/>
       <use x="478.09375" xlink:href="#DejaVuSans-37"/>
       <use x="541.716797" xlink:href="#DejaVuSans-2d"/>
       <use x="577.660156" xlink:href="#DejaVuSans-54"/>
       <use x="638.744141" xlink:href="#DejaVuSans-30"/>
       <use x="702.367188" xlink:href="#DejaVuSans-35"/>
       <use x="765.990234" xlink:href="#DejaVuSans-2d"/>
       <use x="802.074219" xlink:href="#DejaVuSans-49"/>
       <use x="831.566406" xlink:href="#DejaVuSans-4d"/>
       <use x="917.845703" xlink:href="#DejaVuSans-36"/>
      </g>
     </g>
    </g>
    <g id="ytick_4">
     <g id="line2d_28"/>
     <g id="text_29">
      <!-- battenberg -->
      <defs>
       <path d="M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
M 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
L 18.109375 0 
L 9.078125 0 
L 9.078125 75.984375 
L 18.109375 75.984375 
z
" id="DejaVuSans-62"/>
       <path d="M 34.28125 27.484375 
Q 23.390625 27.484375 19.1875 25 
Q 14.984375 22.515625 14.984375 16.5 
Q 14.984375 11.71875 18.140625 8.90625 
Q 21.296875 6.109375 26.703125 6.109375 
Q 34.1875 6.109375 38.703125 11.40625 
Q 43.21875 16.703125 43.21875 25.484375 
L 43.21875 27.484375 
z
M 52.203125 31.203125 
L 52.203125 0 
L 43.21875 0 
L 43.21875 8.296875 
Q 40.140625 3.328125 35.546875 0.953125 
Q 30.953125 -1.421875 24.3125 -1.421875 
Q 15.921875 -1.421875 10.953125 3.296875 
Q 6 8.015625 6 15.921875 
Q 6 25.140625 12.171875 29.828125 
Q 18.359375 34.515625 30.609375 34.515625 
L 43.21875 34.515625 
L 43.21875 35.40625 
Q 43.21875 41.609375 39.140625 45 
Q 35.0625 48.390625 27.6875 48.390625 
Q 23 48.390625 18.546875 47.265625 
Q 14.109375 46.140625 10.015625 43.890625 
L 10.015625 52.203125 
Q 14.9375 54.109375 19.578125 55.046875 
Q 24.21875 56 28.609375 56 
Q 40.484375 56 46.34375 49.84375 
Q 52.203125 43.703125 52.203125 31.203125 
z
" id="DejaVuSans-61"/>
       <path d="M 18.3125 70.21875 
L 18.3125 54.6875 
L 36.8125 54.6875 
L 36.8125 47.703125 
L 18.3125 47.703125 
L 18.3125 18.015625 
Q 18.3125 11.328125 20.140625 9.421875 
Q 21.96875 7.515625 27.59375 7.515625 
L 36.8125 7.515625 
L 36.8125 0 
L 27.59375 0 
Q 17.1875 0 13.234375 3.875 
Q 9.28125 7.765625 9.28125 18.015625 
L 9.28125 47.703125 
L 2.6875 47.703125 
L 2.6875 54.6875 
L 9.28125 54.6875 
L 9.28125 70.21875 
z
" id="DejaVuSans-74"/>
       <path d="M 54.890625 33.015625 
L 54.890625 0 
L 45.90625 0 
L 45.90625 32.71875 
Q 45.90625 40.484375 42.875 44.328125 
Q 39.84375 48.1875 33.796875 48.1875 
Q 26.515625 48.1875 22.3125 43.546875 
Q 18.109375 38.921875 18.109375 30.90625 
L 18.109375 0 
L 9.078125 0 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.1875 
Q 21.34375 51.125 25.703125 53.5625 
Q 30.078125 56 35.796875 56 
Q 45.21875 56 50.046875 50.171875 
Q 54.890625 44.34375 54.890625 33.015625 
z
" id="DejaVuSans-6e"/>
       <path d="M 45.40625 27.984375 
Q 45.40625 37.75 41.375 43.109375 
Q 37.359375 48.484375 30.078125 48.484375 
Q 22.859375 48.484375 18.828125 43.109375 
Q 14.796875 37.75 14.796875 27.984375 
Q 14.796875 18.265625 18.828125 12.890625 
Q 22.859375 7.515625 30.078125 7.515625 
Q 37.359375 7.515625 41.375 12.890625 
Q 45.40625 18.265625 45.40625 27.984375 
z
M 54.390625 6.78125 
Q 54.390625 -7.171875 48.1875 -13.984375 
Q 42 -20.796875 29.203125 -20.796875 
Q 24.46875 -20.796875 20.265625 -20.09375 
Q 16.0625 -19.390625 12.109375 -17.921875 
L 12.109375 -9.1875 
Q 16.0625 -11.328125 19.921875 -12.34375 
Q 23.78125 -13.375 27.78125 -13.375 
Q 36.625 -13.375 41.015625 -8.765625 
Q 45.40625 -4.15625 45.40625 5.171875 
L 45.40625 9.625 
Q 42.625 4.78125 38.28125 2.390625 
Q 33.9375 0 27.875 0 
Q 17.828125 0 11.671875 7.65625 
Q 5.515625 15.328125 5.515625 27.984375 
Q 5.515625 40.671875 11.671875 48.328125 
Q 17.828125 56 27.875 56 
Q 33.9375 56 38.28125 53.609375 
Q 42.625 51.21875 45.40625 46.390625 
L 45.40625 54.6875 
L 54.390625 54.6875 
z
" id="DejaVuSans-67"/>
      </defs>
      <g style="fill:#262626;" transform="translate(57.148217 200.624749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-61"/>
       <use x="124.755859" xlink:href="#DejaVuSans-74"/>
       <use x="163.964844" xlink:href="#DejaVuSans-74"/>
       <use x="203.173828" xlink:href="#DejaVuSans-65"/>
       <use x="264.697266" xlink:href="#DejaVuSans-6e"/>
       <use x="328.076172" xlink:href="#DejaVuSans-62"/>
       <use x="391.552734" xlink:href="#DejaVuSans-65"/>
       <use x="453.076172" xlink:href="#DejaVuSans-72"/>
       <use x="494.173828" xlink:href="#DejaVuSans-67"/>
      </g>
     </g>
    </g>
    <g id="ytick_5">
     <g id="line2d_29"/>
     <g id="text_30">
      <!-- brass -->
      <g style="fill:#262626;" transform="translate(81.106078 254.984749)scale(0.0833 -0.0833)">
       <use xlink:href="#DejaVuSans-62"/>
       <use x="63.476562" xlink:href="#DejaVuSans-72"/>
       <use x="104.589844" xlink:href="#DejaVuSans-61"/>
       <use x="165.869141" xlink:href="#DejaVuSans-73"/>
       <use x="217.96875" xlink:href="#DejaVuSans-73"/>
      </g>
     </g>
    </g>
    <g id="text_31">
     <!-- Samples -->
     <defs>
      <path d="M 53.515625 70.515625 
L 53.515625 60.890625 
Q 47.90625 63.578125 42.921875 64.890625 
Q 37.9375 66.21875 33.296875 66.21875 
Q 25.25 66.21875 20.875 63.09375 
Q 16.5 59.96875 16.5 54.203125 
Q 16.5 49.359375 19.40625 46.890625 
Q 22.3125 44.4375 30.421875 42.921875 
L 36.375 41.703125 
Q 47.40625 39.59375 52.65625 34.296875 
Q 57.90625 29 57.90625 20.125 
Q 57.90625 9.515625 50.796875 4.046875 
Q 43.703125 -1.421875 29.984375 -1.421875 
Q 24.8125 -1.421875 18.96875 -0.25 
Q 13.140625 0.921875 6.890625 3.21875 
L 6.890625 13.375 
Q 12.890625 10.015625 18.65625 8.296875 
Q 24.421875 6.59375 29.984375 6.59375 
Q 38.421875 6.59375 43.015625 9.90625 
Q 47.609375 13.234375 47.609375 19.390625 
Q 47.609375 24.75 44.3125 27.78125 
Q 41.015625 30.8125 33.5 32.328125 
L 27.484375 33.5 
Q 16.453125 35.6875 11.515625 40.375 
Q 6.59375 45.0625 6.59375 53.421875 
Q 6.59375 63.09375 13.40625 68.65625 
Q 20.21875 74.21875 32.171875 74.21875 
Q 37.3125 74.21875 42.625 73.28125 
Q 47.953125 72.359375 53.515625 70.515625 
z
" id="DejaVuSans-53"/>
      <path d="M 18.109375 8.203125 
L 18.109375 -20.796875 
L 9.078125 -20.796875 
L 9.078125 54.6875 
L 18.109375 54.6875 
L 18.109375 46.390625 
Q 20.953125 51.265625 25.265625 53.625 
Q 29.59375 56 35.59375 56 
Q 45.5625 56 51.78125 48.09375 
Q 58.015625 40.1875 58.015625 27.296875 
Q 58.015625 14.40625 51.78125 6.484375 
Q 45.5625 -1.421875 35.59375 -1.421875 
Q 29.59375 -1.421875 25.265625 0.953125 
Q 20.953125 3.328125 18.109375 8.203125 
z
M 48.6875 27.296875 
Q 48.6875 37.203125 44.609375 42.84375 
Q 40.53125 48.484375 33.40625 48.484375 
Q 26.265625 48.484375 22.1875 42.84375 
Q 18.109375 37.203125 18.109375 27.296875 
Q 18.109375 17.390625 22.1875 11.75 
Q 26.265625 6.109375 33.40625 6.109375 
Q 40.53125 6.109375 44.609375 11.75 
Q 48.6875 17.390625 48.6875 27.296875 
z
" id="DejaVuSans-70"/>
      <path d="M 9.421875 75.984375 
L 18.40625 75.984375 
L 18.40625 0 
L 9.421875 0 
z
" id="DejaVuSans-6c"/>
     </defs>
     <g style="fill:#262626;" transform="translate(15.558281 166.588437)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-53"/>
      <use x="63.476562" xlink:href="#DejaVuSans-61"/>
      <use x="124.755859" xlink:href="#DejaVuSans-6d"/>
      <use x="222.167969" xlink:href="#DejaVuSans-70"/>
      <use x="285.644531" xlink:href="#DejaVuSans-6c"/>
      <use x="313.427734" xlink:href="#DejaVuSans-65"/>
      <use x="374.951172" xlink:href="#DejaVuSans-73"/>
     </g>
    </g>
   </g>
   <g id="BrokenBarHCollection_1">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 7.2 
L 111.019565 61.56 
L 114.390446 61.56 
L 114.390446 7.2 
L 111.019565 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 7.2 
L 114.607323 61.56 
L 115.766838 61.56 
L 115.766838 7.2 
L 114.607323 7.2 
z
" style="fill:#5050d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 7.2 
L 116.474334 61.56 
L 151.854697 61.56 
L 151.854697 7.2 
L 116.474334 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_2">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 7.2 
L 153.192895 61.56 
L 193.121401 61.56 
L 193.121401 7.2 
L 153.192895 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_3">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 7.2 
L 193.429592 61.56 
L 225.761718 61.56 
L 225.761718 7.2 
L 193.429592 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_4">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 7.2 
L 226.618581 61.56 
L 257.280911 61.56 
L 257.280911 7.2 
L 226.618581 7.2 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.806331 7.2 
L 257.806331 61.56 
L 258.291836 61.56 
L 258.291836 7.2 
L 257.806331 7.2 
z
" style="fill:#6060d4;"/>
   </g>
   <g id="BrokenBarHCollection_5">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 7.2 
L 258.451581 61.56 
L 264.954048 61.56 
L 264.954048 7.2 
L 258.451581 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.955027 7.2 
L 264.955027 61.56 
L 264.968025 61.56 
L 264.968025 7.2 
L 264.955027 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 265.199965 7.2 
L 265.199965 61.56 
L 268.312717 61.56 
L 268.312717 7.2 
L 265.199965 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 7.2 
L 269.739011 61.56 
L 270.602549 61.56 
L 270.602549 7.2 
L 269.739011 7.2 
z
" style="fill:#5d5dd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.011699 7.2 
L 271.011699 61.56 
L 288.615161 61.56 
L 288.615161 7.2 
L 271.011699 7.2 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_6">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 7.2 
L 288.820016 61.56 
L 300.922698 61.56 
L 300.922698 7.2 
L 288.820016 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 7.2 
L 301.600291 61.56 
L 302.60843 61.56 
L 302.60843 7.2 
L 301.600291 7.2 
z
" style="fill:#b2b2e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 7.2 
L 302.649075 61.56 
L 305.577669 61.56 
L 305.577669 7.2 
L 302.649075 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 7.2 
L 306.53976 61.56 
L 308.48497 61.56 
L 308.48497 7.2 
L 306.53976 7.2 
z
" style="fill:#5353d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.48629 7.2 
L 308.48629 61.56 
L 317.398358 61.56 
L 317.398358 7.2 
L 308.48629 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_7">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 7.2 
L 317.715519 61.56 
L 317.798362 61.56 
L 317.798362 7.2 
L 317.715519 7.2 
z
" style="fill:#e9b7b7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.877833 7.2 
L 317.877833 61.56 
L 321.290202 61.56 
L 321.290202 7.2 
L 317.877833 7.2 
z
" style="fill:#ce4444;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.341562 7.2 
L 321.341562 61.56 
L 344.008473 61.56 
L 344.008473 7.2 
L 321.341562 7.2 
z
" style="fill:#e6abab;"/>
   </g>
   <g id="BrokenBarHCollection_8">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 7.2 
L 344.216853 61.56 
L 365.232264 61.56 
L 365.232264 7.2 
L 344.216853 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 7.2 
L 365.646321 61.56 
L 368.564309 61.56 
L 368.564309 7.2 
L 365.646321 7.2 
z
" style="fill:#e7b0b0;"/>
   </g>
   <g id="BrokenBarHCollection_9">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 7.2 
L 368.7291 61.56 
L 369.512101 61.56 
L 369.512101 7.2 
L 368.7291 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.517508 7.2 
L 369.517508 61.56 
L 369.518124 61.56 
L 369.518124 7.2 
L 369.517508 7.2 
z
" style="fill:#e4a4a4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 7.2 
L 369.573367 61.56 
L 382.810635 61.56 
L 382.810635 7.2 
L 369.573367 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.296829 7.2 
L 383.296829 61.56 
L 383.355609 61.56 
L 383.355609 7.2 
L 383.296829 7.2 
z
" style="fill:#8c8cde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.17047 7.2 
L 384.17047 61.56 
L 392.107267 61.56 
L 392.107267 7.2 
L 384.17047 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_10">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 7.2 
L 392.583985 61.56 
L 414.83696 61.56 
L 414.83696 7.2 
L 392.583985 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_11">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 7.2 
L 415.142546 61.56 
L 437.441446 61.56 
L 437.441446 7.2 
L 415.142546 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_12">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 7.2 
L 437.750937 61.56 
L 449.295706 61.56 
L 449.295706 7.2 
L 437.750937 7.2 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 7.2 
L 450.72936 61.56 
L 460.034121 61.56 
L 460.034121 7.2 
L 450.72936 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_13">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 7.2 
L 463.652226 61.56 
L 467.98385 61.56 
L 467.98385 7.2 
L 463.652226 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.326807 7.2 
L 468.326807 61.56 
L 468.336214 61.56 
L 468.336214 7.2 
L 468.326807 7.2 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.336686 7.2 
L 468.336686 61.56 
L 478.765097 61.56 
L 478.765097 7.2 
L 468.336686 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_14">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 7.2 
L 482.846724 61.56 
L 497.195548 61.56 
L 497.195548 7.2 
L 482.846724 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_15">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 7.2 
L 501.824206 61.56 
L 504.480831 61.56 
L 504.480831 7.2 
L 501.824206 7.2 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.481111 7.2 
L 504.481111 61.56 
L 508.002235 61.56 
L 508.002235 7.2 
L 504.481111 7.2 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.121683 7.2 
L 508.121683 61.56 
L 514.175084 61.56 
L 514.175084 7.2 
L 508.121683 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_16">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 7.2 
L 514.64034 61.56 
L 529.695113 61.56 
L 529.695113 7.2 
L 514.64034 7.2 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_17">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 7.2 
L 529.783317 61.56 
L 541.322677 61.56 
L 541.322677 7.2 
L 529.783317 7.2 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.485043 7.2 
L 541.485043 61.56 
L 541.524165 61.56 
L 541.524165 7.2 
L 541.485043 7.2 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.996595 7.2 
L 541.996595 61.56 
L 543.312021 61.56 
L 543.312021 7.2 
L 541.996595 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_18">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 7.2 
L 543.502642 61.56 
L 555.856459 61.56 
L 555.856459 7.2 
L 543.502642 7.2 
z
" style="fill:#6969d6;"/>
   </g>
   <g id="BrokenBarHCollection_19">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 7.2 
L 556.667579 61.56 
L 566.240523 61.56 
L 566.240523 7.2 
L 556.667579 7.2 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_20">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 7.2 
L 566.437738 61.56 
L 576.513661 61.56 
L 576.513661 7.2 
L 566.437738 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_21">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 7.2 
L 579.924517 61.56 
L 584.597146 61.56 
L 584.597146 7.2 
L 579.924517 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_22">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 7.2 
L 588.204868 61.56 
L 588.788782 61.56 
L 588.788782 7.2 
L 588.204868 7.2 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.056152 7.2 
L 589.056152 61.56 
L 589.064076 61.56 
L 589.064076 7.2 
L 589.056152 7.2 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.285131 7.2 
L 589.285131 61.56 
L 589.631742 61.56 
L 589.631742 7.2 
L 589.285131 7.2 
z
" style="fill:#afafe7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.887065 7.2 
L 589.887065 61.56 
L 590.197891 61.56 
L 590.197891 7.2 
L 589.887065 7.2 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.682849 7.2 
L 590.682849 61.56 
L 593.289336 61.56 
L 593.289336 7.2 
L 590.682849 7.2 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_23">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 7.2 
L 593.679182 61.56 
L 618.747061 61.56 
L 618.747061 7.2 
L 593.679182 7.2 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_24">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 61.56 
L 111.019565 170.28 
L 114.390446 170.28 
L 114.390446 61.56 
L 111.019565 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.607323 61.56 
L 114.607323 170.28 
L 115.766838 170.28 
L 115.766838 61.56 
L 114.607323 61.56 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.474334 61.56 
L 116.474334 170.28 
L 151.970825 170.28 
L 151.970825 61.56 
L 116.474334 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_25">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 61.56 
L 153.192895 170.28 
L 193.121401 170.28 
L 193.121401 61.56 
L 153.192895 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_26">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 61.56 
L 193.429592 170.28 
L 225.761718 170.28 
L 225.761718 61.56 
L 193.429592 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_27">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 61.56 
L 226.618581 170.28 
L 258.291836 170.28 
L 258.291836 61.56 
L 226.618581 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_28">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 61.56 
L 258.451581 170.28 
L 268.312717 170.28 
L 268.312717 61.56 
L 258.451581 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.739011 61.56 
L 269.739011 170.28 
L 269.750862 170.28 
L 269.750862 61.56 
L 269.739011 61.56 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.884516 61.56 
L 269.884516 170.28 
L 288.615161 170.28 
L 288.615161 61.56 
L 269.884516 61.56 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_29">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 61.56 
L 288.820016 170.28 
L 300.922698 170.28 
L 300.922698 61.56 
L 288.820016 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.600291 61.56 
L 301.600291 170.28 
L 302.60843 170.28 
L 302.60843 61.56 
L 301.600291 61.56 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.649075 61.56 
L 302.649075 170.28 
L 305.577669 170.28 
L 305.577669 61.56 
L 302.649075 61.56 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.53976 61.56 
L 306.53976 170.28 
L 308.48629 170.28 
L 308.48629 61.56 
L 306.53976 61.56 
z
" style="fill:#6b6bd6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486955 61.56 
L 308.486955 170.28 
L 317.398358 170.28 
L 317.398358 61.56 
L 308.486955 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_30">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 61.56 
L 317.715519 170.28 
L 344.008473 170.28 
L 344.008473 61.56 
L 317.715519 61.56 
z
" style="fill:#e7afaf;"/>
   </g>
   <g id="BrokenBarHCollection_31">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 61.56 
L 344.216853 170.28 
L 365.232264 170.28 
L 365.232264 61.56 
L 344.216853 61.56 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.646321 61.56 
L 365.646321 170.28 
L 368.564309 170.28 
L 368.564309 61.56 
L 365.646321 61.56 
z
" style="fill:#e8b4b4;"/>
   </g>
   <g id="BrokenBarHCollection_32">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 61.56 
L 368.7291 170.28 
L 392.107267 170.28 
L 392.107267 61.56 
L 368.7291 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_33">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 61.56 
L 392.583985 170.28 
L 414.83696 170.28 
L 414.83696 61.56 
L 392.583985 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_34">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 61.56 
L 415.142546 170.28 
L 437.441446 170.28 
L 437.441446 61.56 
L 415.142546 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_35">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 61.56 
L 437.750937 170.28 
L 448.911627 170.28 
L 448.911627 61.56 
L 437.750937 61.56 
z
" style="fill:#e8b3b3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.140439 61.56 
L 449.140439 170.28 
L 449.295706 170.28 
L 449.295706 61.56 
L 449.140439 61.56 
z
" style="fill:#cb3939;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.72936 61.56 
L 450.72936 170.28 
L 460.034121 170.28 
L 460.034121 61.56 
L 450.72936 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_36">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 61.56 
L 463.652226 170.28 
L 478.765097 170.28 
L 478.765097 61.56 
L 463.652226 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_37">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 61.56 
L 482.846724 170.28 
L 497.195548 170.28 
L 497.195548 61.56 
L 482.846724 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_38">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 61.56 
L 501.824206 170.28 
L 502.967435 170.28 
L 502.967435 61.56 
L 501.824206 61.56 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.611321 61.56 
L 503.611321 170.28 
L 503.908339 170.28 
L 503.908339 61.56 
L 503.611321 61.56 
z
" style="fill:#e8b4b4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.062756 61.56 
L 504.062756 170.28 
L 514.175084 170.28 
L 514.175084 61.56 
L 504.062756 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_39">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 61.56 
L 514.64034 170.28 
L 529.695113 170.28 
L 529.695113 61.56 
L 514.64034 61.56 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_40">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 61.56 
L 529.783317 170.28 
L 543.312021 170.28 
L 543.312021 61.56 
L 529.783317 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_41">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 61.56 
L 543.502642 170.28 
L 555.856459 170.28 
L 555.856459 61.56 
L 543.502642 61.56 
z
" style="fill:#7777d9;"/>
   </g>
   <g id="BrokenBarHCollection_42">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 61.56 
L 556.667579 170.28 
L 566.240523 170.28 
L 566.240523 61.56 
L 556.667579 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_43">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 61.56 
L 566.437738 170.28 
L 576.832477 170.28 
L 576.832477 61.56 
L 566.437738 61.56 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_44">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 61.56 
L 579.924517 170.28 
L 584.597146 170.28 
L 584.597146 61.56 
L 579.924517 61.56 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_45">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 61.56 
L 588.204868 170.28 
L 593.289336 170.28 
L 593.289336 61.56 
L 588.204868 61.56 
z
" style="fill:#7171d8;"/>
   </g>
   <g id="BrokenBarHCollection_46">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 61.56 
L 593.679182 170.28 
L 619.240077 170.28 
L 619.240077 61.56 
L 593.679182 61.56 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_47">
    <path clip-path="url(#p9901fb19d8)" d="M 111.019565 115.92 
L 111.019565 279 
L 151.970825 279 
L 151.970825 115.92 
L 111.019565 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_48">
    <path clip-path="url(#p9901fb19d8)" d="M 153.192895 115.92 
L 153.192895 279 
L 175.053998 279 
L 175.053998 115.92 
L 153.192895 115.92 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.355971 115.92 
L 175.355971 279 
L 177.919584 279 
L 177.919584 115.92 
L 175.355971 115.92 
z
" style="fill:#f2f2fa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.344299 115.92 
L 178.344299 279 
L 193.121401 279 
L 193.121401 115.92 
L 178.344299 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_49">
    <path clip-path="url(#p9901fb19d8)" d="M 193.429592 115.92 
L 193.429592 279 
L 198.092006 279 
L 198.092006 115.92 
L 193.429592 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.326415 115.92 
L 198.326415 279 
L 198.340086 279 
L 198.340086 115.92 
L 198.326415 115.92 
z
" style="fill:#eeeef8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.3406 115.92 
L 198.3406 279 
L 225.761718 279 
L 225.761718 115.92 
L 198.3406 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_50">
    <path clip-path="url(#p9901fb19d8)" d="M 226.618581 115.92 
L 226.618581 279 
L 258.291836 279 
L 258.291836 115.92 
L 226.618581 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_51">
    <path clip-path="url(#p9901fb19d8)" d="M 258.451581 115.92 
L 258.451581 279 
L 288.615161 279 
L 288.615161 115.92 
L 258.451581 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_52">
    <path clip-path="url(#p9901fb19d8)" d="M 288.820016 115.92 
L 288.820016 279 
L 317.398358 279 
L 317.398358 115.92 
L 288.820016 115.92 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_53">
    <path clip-path="url(#p9901fb19d8)" d="M 317.715519 115.92 
L 317.715519 279 
L 344.008473 279 
L 344.008473 115.92 
L 317.715519 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_54">
    <path clip-path="url(#p9901fb19d8)" d="M 344.216853 115.92 
L 344.216853 279 
L 368.564309 279 
L 368.564309 115.92 
L 344.216853 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_55">
    <path clip-path="url(#p9901fb19d8)" d="M 368.7291 115.92 
L 368.7291 279 
L 369.518124 279 
L 369.518124 115.92 
L 368.7291 115.92 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.573367 115.92 
L 369.573367 279 
L 369.575331 279 
L 369.575331 115.92 
L 369.573367 115.92 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.584509 115.92 
L 369.584509 279 
L 392.107267 279 
L 392.107267 115.92 
L 369.584509 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_56">
    <path clip-path="url(#p9901fb19d8)" d="M 392.583985 115.92 
L 392.583985 279 
L 414.83696 279 
L 414.83696 115.92 
L 392.583985 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_57">
    <path clip-path="url(#p9901fb19d8)" d="M 415.142546 115.92 
L 415.142546 279 
L 437.441446 279 
L 437.441446 115.92 
L 415.142546 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_58">
    <path clip-path="url(#p9901fb19d8)" d="M 437.750937 115.92 
L 437.750937 279 
L 460.034121 279 
L 460.034121 115.92 
L 437.750937 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_59">
    <path clip-path="url(#p9901fb19d8)" d="M 463.652226 115.92 
L 463.652226 279 
L 478.765097 279 
L 478.765097 115.92 
L 463.652226 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_60">
    <path clip-path="url(#p9901fb19d8)" d="M 482.846724 115.92 
L 482.846724 279 
L 497.195548 279 
L 497.195548 115.92 
L 482.846724 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_61">
    <path clip-path="url(#p9901fb19d8)" d="M 501.824206 115.92 
L 501.824206 279 
L 514.175084 279 
L 514.175084 115.92 
L 501.824206 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_62">
    <path clip-path="url(#p9901fb19d8)" d="M 514.64034 115.92 
L 514.64034 279 
L 529.695113 279 
L 529.695113 115.92 
L 514.64034 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_63">
    <path clip-path="url(#p9901fb19d8)" d="M 529.783317 115.92 
L 529.783317 279 
L 543.312021 279 
L 543.312021 115.92 
L 529.783317 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_64">
    <path clip-path="url(#p9901fb19d8)" d="M 543.502642 115.92 
L 543.502642 279 
L 555.856459 279 
L 555.856459 115.92 
L 543.502642 115.92 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_65">
    <path clip-path="url(#p9901fb19d8)" d="M 556.667579 115.92 
L 556.667579 279 
L 566.240523 279 
L 566.240523 115.92 
L 556.667579 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_66">
    <path clip-path="url(#p9901fb19d8)" d="M 566.437738 115.92 
L 566.437738 279 
L 576.832477 279 
L 576.832477 115.92 
L 566.437738 115.92 
z
" style="fill:#fffefe;"/>
   </g>
   <g id="BrokenBarHCollection_67">
    <path clip-path="url(#p9901fb19d8)" d="M 579.924517 115.92 
L 579.924517 279 
L 584.597146 279 
L 584.597146 115.92 
L 579.924517 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_68">
    <path clip-path="url(#p9901fb19d8)" d="M 588.204868 115.92 
L 588.204868 279 
L 593.289336 279 
L 593.289336 115.92 
L 588.204868 115.92 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_69">
    <path clip-path="url(#p9901fb19d8)" d="M 593.679182 115.92 
L 593.679182 279 
L 619.240077 279 
L 619.240077 115.92 
L 593.679182 115.92 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_70">
    <path clip-path="url(#p9901fb19d8)" d="M 110.732517 170.28 
L 110.732517 387.72 
L 114.49766 387.72 
L 114.49766 170.28 
L 110.732517 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497699 170.28 
L 114.497699 387.72 
L 114.767892 387.72 
L 114.767892 170.28 
L 114.497699 170.28 
z
" style="fill:#3838cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768273 170.28 
L 114.768273 387.72 
L 115.076345 387.72 
L 115.076345 170.28 
L 114.768273 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076722 170.28 
L 115.076722 387.72 
L 115.913829 387.72 
L 115.913829 170.28 
L 115.076722 170.28 
z
" style="fill:#3737cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.91422 170.28 
L 115.91422 387.72 
L 152.391167 387.72 
L 152.391167 170.28 
L 115.91422 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_71">
    <path clip-path="url(#p9901fb19d8)" d="M 152.414637 170.28 
L 152.414637 387.72 
L 191.814503 387.72 
L 191.814503 170.28 
L 152.414637 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.814762 170.28 
L 191.814762 387.72 
L 192.069828 387.72 
L 192.069828 170.28 
L 191.814762 170.28 
z
" style="fill:#a9a9e5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.074783 170.28 
L 192.074783 387.72 
L 192.178653 387.72 
L 192.178653 170.28 
L 192.074783 170.28 
z
" style="fill:#efeff9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.189877 170.28 
L 192.189877 387.72 
L 192.413847 387.72 
L 192.413847 170.28 
L 192.189877 170.28 
z
" style="fill:#2b2bc8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.4146 170.28 
L 192.4146 387.72 
L 193.152251 387.72 
L 193.152251 170.28 
L 192.4146 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_72">
    <path clip-path="url(#p9901fb19d8)" d="M 193.1966 170.28 
L 193.1966 387.72 
L 226.354821 387.72 
L 226.354821 170.28 
L 193.1966 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_73">
    <path clip-path="url(#p9901fb19d8)" d="M 226.398813 170.28 
L 226.398813 387.72 
L 257.860212 387.72 
L 257.860212 170.28 
L 226.398813 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.872858 170.28 
L 257.872858 387.72 
L 257.906904 387.72 
L 257.906904 170.28 
L 257.872858 170.28 
z
" style="fill:#2c2cc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907281 170.28 
L 257.907281 387.72 
L 258.378942 387.72 
L 258.378942 170.28 
L 257.907281 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_74">
    <path clip-path="url(#p9901fb19d8)" d="M 258.557753 170.28 
L 258.557753 387.72 
L 269.508015 387.72 
L 269.508015 170.28 
L 258.557753 170.28 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509871 170.28 
L 269.509871 387.72 
L 270.950289 387.72 
L 270.950289 170.28 
L 269.509871 170.28 
z
" style="fill:#3b3bcc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.951029 170.28 
L 270.951029 387.72 
L 273.967422 387.72 
L 273.967422 170.28 
L 270.951029 170.28 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.971654 170.28 
L 273.971654 387.72 
L 274.235702 387.72 
L 274.235702 170.28 
L 273.971654 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.237182 170.28 
L 274.237182 387.72 
L 288.733363 387.72 
L 288.733363 170.28 
L 274.237182 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_75">
    <path clip-path="url(#p9901fb19d8)" d="M 288.790489 170.28 
L 288.790489 387.72 
L 301.463707 387.72 
L 301.463707 170.28 
L 288.790489 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.467988 170.28 
L 301.467988 387.72 
L 302.636666 387.72 
L 302.636666 170.28 
L 301.467988 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.647085 170.28 
L 302.647085 387.72 
L 302.954433 387.72 
L 302.954433 170.28 
L 302.647085 170.28 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.955568 170.28 
L 302.955568 387.72 
L 303.508231 387.72 
L 303.508231 170.28 
L 302.955568 170.28 
z
" style="fill:#2e2ec9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.518351 170.28 
L 303.518351 387.72 
L 304.015885 387.72 
L 304.015885 170.28 
L 303.518351 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.017424 170.28 
L 304.017424 387.72 
L 304.50692 387.72 
L 304.50692 170.28 
L 304.017424 170.28 
z
" style="fill:#3030c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506959 170.28 
L 304.506959 387.72 
L 306.169781 387.72 
L 306.169781 170.28 
L 304.506959 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.182146 170.28 
L 306.182146 387.72 
L 308.011533 387.72 
L 308.011533 170.28 
L 306.182146 170.28 
z
" style="fill:#2f2fc9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011842 170.28 
L 308.011842 387.72 
L 308.191175 387.72 
L 308.191175 170.28 
L 308.011842 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191555 170.28 
L 308.191555 387.72 
L 308.486252 387.72 
L 308.486252 170.28 
L 308.191555 170.28 
z
" style="fill:#3232ca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486388 170.28 
L 308.486388 387.72 
L 317.418935 387.72 
L 317.418935 170.28 
L 308.486388 170.28 
z
" style="fill:#fbfbfd;"/>
   </g>
   <g id="BrokenBarHCollection_76">
    <path clip-path="url(#p9901fb19d8)" d="M 317.448645 170.28 
L 317.448645 387.72 
L 344.121125 387.72 
L 344.121125 170.28 
L 317.448645 170.28 
z
" style="fill:#e8b3b3;"/>
   </g>
   <g id="BrokenBarHCollection_77">
    <path clip-path="url(#p9901fb19d8)" d="M 344.154217 170.28 
L 344.154217 387.72 
L 365.358415 387.72 
L 365.358415 170.28 
L 344.154217 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.364598 170.28 
L 365.364598 387.72 
L 367.307833 387.72 
L 367.307833 170.28 
L 365.364598 170.28 
z
" style="fill:#e6acac;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.308153 170.28 
L 367.308153 387.72 
L 367.503452 387.72 
L 367.503452 170.28 
L 367.308153 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503975 170.28 
L 367.503975 387.72 
L 368.653254 387.72 
L 368.653254 170.28 
L 367.503975 170.28 
z
" style="fill:#e9b7b7;"/>
   </g>
   <g id="BrokenBarHCollection_78">
    <path clip-path="url(#p9901fb19d8)" d="M 368.69434 170.28 
L 368.69434 387.72 
L 383.624676 387.72 
L 383.624676 170.28 
L 368.69434 170.28 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625528 170.28 
L 383.625528 387.72 
L 383.661673 387.72 
L 383.661673 170.28 
L 383.625528 170.28 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662489 170.28 
L 383.662489 387.72 
L 392.316686 387.72 
L 392.316686 170.28 
L 383.662489 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_79">
    <path clip-path="url(#p9901fb19d8)" d="M 392.346424 170.28 
L 392.346424 387.72 
L 395.782185 387.72 
L 395.782185 170.28 
L 392.346424 170.28 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.783252 170.28 
L 395.783252 387.72 
L 395.788255 387.72 
L 395.788255 170.28 
L 395.783252 170.28 
z
" style="fill:#2929c8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788409 170.28 
L 395.788409 387.72 
L 398.822562 387.72 
L 398.822562 170.28 
L 395.788409 170.28 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.823289 170.28 
L 398.823289 387.72 
L 398.888134 387.72 
L 398.888134 170.28 
L 398.823289 170.28 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.888642 170.28 
L 398.888642 387.72 
L 415.005311 387.72 
L 415.005311 170.28 
L 398.888642 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_80">
    <path clip-path="url(#p9901fb19d8)" d="M 415.094738 170.28 
L 415.094738 387.72 
L 437.684388 387.72 
L 437.684388 170.28 
L 415.094738 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_81">
    <path clip-path="url(#p9901fb19d8)" d="M 437.716316 170.28 
L 437.716316 387.72 
L 449.018201 387.72 
L 449.018201 170.28 
L 437.716316 170.28 
z
" style="fill:#e5aaaa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.027649 170.28 
L 449.027649 387.72 
L 450.221487 387.72 
L 450.221487 170.28 
L 449.027649 170.28 
z
" style="fill:#cc3c3c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221763 170.28 
L 450.221763 387.72 
L 460.129444 387.72 
L 460.129444 170.28 
L 450.221763 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_82">
    <path clip-path="url(#p9901fb19d8)" d="M 463.391449 170.28 
L 463.391449 387.72 
L 479.415931 387.72 
L 479.415931 170.28 
L 463.391449 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_83">
    <path clip-path="url(#p9901fb19d8)" d="M 482.863709 170.28 
L 482.863709 387.72 
L 497.422735 387.72 
L 497.422735 170.28 
L 482.863709 170.28 
z
" style="fill:#ffffff;"/>
   </g>
   <g id="BrokenBarHCollection_84">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781985 170.28 
L 500.781985 387.72 
L 503.23667 387.72 
L 503.23667 170.28 
L 500.781985 170.28 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236809 170.28 
L 503.236809 387.72 
L 503.946262 387.72 
L 503.946262 170.28 
L 503.236809 170.28 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948559 170.28 
L 503.948559 387.72 
L 504.456444 387.72 
L 504.456444 170.28 
L 503.948559 170.28 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.483244 170.28 
L 504.483244 387.72 
L 504.598322 387.72 
L 504.598322 170.28 
L 504.483244 170.28 
z
" style="fill:#4747ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.608391 170.28 
L 504.608391 387.72 
L 514.59768 387.72 
L 514.59768 170.28 
L 504.608391 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_85">
    <path clip-path="url(#p9901fb19d8)" d="M 514.635095 170.28 
L 514.635095 387.72 
L 529.713499 387.72 
L 529.713499 170.28 
L 514.635095 170.28 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="BrokenBarHCollection_86">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764399 170.28 
L 529.764399 387.72 
L 543.179433 387.72 
L 543.179433 170.28 
L 529.764399 170.28 
z
" style="fill:#fcfcfe;"/>
   </g>
   <g id="BrokenBarHCollection_87">
    <path clip-path="url(#p9901fb19d8)" d="M 543.402159 170.28 
L 543.402159 387.72 
L 556.4652 387.72 
L 556.4652 170.28 
L 543.402159 170.28 
z
" style="fill:#3838cb;"/>
   </g>
   <g id="BrokenBarHCollection_88">
    <path clip-path="url(#p9901fb19d8)" d="M 556.512332 170.28 
L 556.512332 387.72 
L 566.37257 387.72 
L 566.37257 170.28 
L 556.512332 170.28 
z
" style="fill:#fcfcfd;"/>
   </g>
   <g id="BrokenBarHCollection_89">
    <path clip-path="url(#p9901fb19d8)" d="M 569.734022 170.28 
L 569.734022 387.72 
L 576.938405 387.72 
L 576.938405 170.28 
L 569.734022 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_90">
    <path clip-path="url(#p9901fb19d8)" d="M 579.500933 170.28 
L 579.500933 387.72 
L 585.005018 387.72 
L 585.005018 170.28 
L 579.500933 170.28 
z
" style="fill:#fefefe;"/>
   </g>
   <g id="BrokenBarHCollection_91">
    <path clip-path="url(#p9901fb19d8)" d="M 587.79365 170.28 
L 587.79365 387.72 
L 591.055437 387.72 
L 591.055437 170.28 
L 587.79365 170.28 
z
" style="fill:#3535cb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.058191 170.28 
L 591.058191 387.72 
L 591.113133 387.72 
L 591.113133 170.28 
L 591.058191 170.28 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.123311 170.28 
L 591.123311 387.72 
L 593.39419 387.72 
L 593.39419 170.28 
L 591.123311 170.28 
z
" style="fill:#3636cb;"/>
   </g>
   <g id="BrokenBarHCollection_92">
    <path clip-path="url(#p9901fb19d8)" d="M 593.847671 170.28 
L 593.847671 387.72 
L 619.640085 387.72 
L 619.640085 170.28 
L 593.847671 170.28 
z
" style="fill:#fefeff;"/>
   </g>
   <g id="BrokenBarHCollection_93">
    <path clip-path="url(#p9901fb19d8)" d="M 110.622326 224.64 
L 110.622326 496.44 
L 110.660815 496.44 
L 110.660815 224.64 
L 110.622326 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.668865 224.64 
L 110.668865 496.44 
L 110.689828 496.44 
L 110.689828 224.64 
L 110.668865 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.689828 224.64 
L 110.689828 496.44 
L 110.708527 496.44 
L 110.708527 224.64 
L 110.689828 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.708947 224.64 
L 110.708947 496.44 
L 110.922439 496.44 
L 110.922439 224.64 
L 110.708947 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 110.922439 224.64 
L 110.922439 496.44 
L 111.038912 496.44 
L 111.038912 224.64 
L 110.922439 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.040253 224.64 
L 111.040253 496.44 
L 111.142303 496.44 
L 111.142303 224.64 
L 111.040253 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.142303 224.64 
L 111.142303 496.44 
L 111.312862 496.44 
L 111.312862 224.64 
L 111.142303 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.312862 224.64 
L 111.312862 496.44 
L 111.57784 496.44 
L 111.57784 224.64 
L 111.312862 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 111.57784 224.64 
L 111.57784 496.44 
L 112.708694 496.44 
L 112.708694 224.64 
L 111.57784 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.708694 224.64 
L 112.708694 496.44 
L 112.789529 496.44 
L 112.789529 224.64 
L 112.708694 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.789529 224.64 
L 112.789529 496.44 
L 112.800765 496.44 
L 112.800765 224.64 
L 112.789529 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.810241 224.64 
L 112.810241 496.44 
L 112.839086 496.44 
L 112.839086 224.64 
L 112.810241 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.842776 224.64 
L 112.842776 496.44 
L 112.863153 496.44 
L 112.863153 224.64 
L 112.842776 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.890153 224.64 
L 112.890153 496.44 
L 112.902228 496.44 
L 112.902228 224.64 
L 112.890153 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 112.912123 224.64 
L 112.912123 496.44 
L 113.212572 496.44 
L 113.212572 224.64 
L 112.912123 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.212572 224.64 
L 113.212572 496.44 
L 113.326864 496.44 
L 113.326864 224.64 
L 113.212572 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.326864 224.64 
L 113.326864 496.44 
L 113.562829 496.44 
L 113.562829 224.64 
L 113.326864 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.562829 224.64 
L 113.562829 496.44 
L 113.79762 496.44 
L 113.79762 224.64 
L 113.562829 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.79762 224.64 
L 113.79762 496.44 
L 113.926503 496.44 
L 113.926503 224.64 
L 113.79762 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 113.926503 224.64 
L 113.926503 496.44 
L 114.129346 496.44 
L 114.129346 224.64 
L 113.926503 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.129346 224.64 
L 114.129346 496.44 
L 114.339651 496.44 
L 114.339651 224.64 
L 114.129346 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.339651 224.64 
L 114.339651 496.44 
L 114.497632 496.44 
L 114.497632 224.64 
L 114.339651 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.497632 224.64 
L 114.497632 496.44 
L 114.569663 496.44 
L 114.569663 224.64 
L 114.497632 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.569663 224.64 
L 114.569663 496.44 
L 114.670539 496.44 
L 114.670539 224.64 
L 114.569663 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.688148 224.64 
L 114.688148 496.44 
L 114.714562 496.44 
L 114.714562 224.64 
L 114.688148 224.64 
z
" style="fill:#6f6fd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.715065 224.64 
L 114.715065 496.44 
L 114.762191 496.44 
L 114.762191 224.64 
L 114.715065 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.768061 224.64 
L 114.768061 496.44 
L 114.807304 496.44 
L 114.807304 224.64 
L 114.768061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 114.807304 224.64 
L 114.807304 496.44 
L 115.076559 496.44 
L 115.076559 224.64 
L 114.807304 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.076559 224.64 
L 115.076559 496.44 
L 115.384722 496.44 
L 115.384722 224.64 
L 115.076559 224.64 
z
" style="fill:#7878d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.384722 224.64 
L 115.384722 496.44 
L 115.581192 496.44 
L 115.581192 224.64 
L 115.384722 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.581192 224.64 
L 115.581192 496.44 
L 115.802566 496.44 
L 115.802566 224.64 
L 115.581192 224.64 
z
" style="fill:#5c5cd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.802566 224.64 
L 115.802566 496.44 
L 115.914008 496.44 
L 115.914008 224.64 
L 115.802566 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.914008 224.64 
L 115.914008 496.44 
L 115.984445 496.44 
L 115.984445 224.64 
L 115.914008 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 115.984445 224.64 
L 115.984445 496.44 
L 116.012536 496.44 
L 116.012536 224.64 
L 115.984445 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.012536 224.64 
L 116.012536 496.44 
L 116.312314 496.44 
L 116.312314 224.64 
L 116.012536 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.312314 224.64 
L 116.312314 496.44 
L 116.48673 496.44 
L 116.48673 224.64 
L 116.312314 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.48673 224.64 
L 116.48673 496.44 
L 116.596327 496.44 
L 116.596327 224.64 
L 116.48673 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 116.596327 224.64 
L 116.596327 496.44 
L 117.200578 496.44 
L 117.200578 224.64 
L 116.596327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.200578 224.64 
L 117.200578 496.44 
L 117.263133 496.44 
L 117.263133 224.64 
L 117.200578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.263133 224.64 
L 117.263133 496.44 
L 117.853799 496.44 
L 117.853799 224.64 
L 117.263133 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 117.853799 224.64 
L 117.853799 496.44 
L 118.177391 496.44 
L 118.177391 224.64 
L 117.853799 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.177391 224.64 
L 118.177391 496.44 
L 118.457631 496.44 
L 118.457631 224.64 
L 118.177391 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.457631 224.64 
L 118.457631 496.44 
L 118.555908 496.44 
L 118.555908 224.64 
L 118.457631 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 118.555908 224.64 
L 118.555908 496.44 
L 119.036642 496.44 
L 119.036642 224.64 
L 118.555908 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.036642 224.64 
L 119.036642 496.44 
L 119.219695 496.44 
L 119.219695 224.64 
L 119.036642 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.219695 224.64 
L 119.219695 496.44 
L 119.931614 496.44 
L 119.931614 224.64 
L 119.219695 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 119.931614 224.64 
L 119.931614 496.44 
L 120.01572 496.44 
L 120.01572 224.64 
L 119.931614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.016223 224.64 
L 120.016223 496.44 
L 120.472639 496.44 
L 120.472639 224.64 
L 120.016223 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.472639 224.64 
L 120.472639 496.44 
L 120.529576 496.44 
L 120.529576 224.64 
L 120.472639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.530163 224.64 
L 120.530163 496.44 
L 120.702483 496.44 
L 120.702483 224.64 
L 120.530163 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 120.702483 224.64 
L 120.702483 496.44 
L 121.025153 496.44 
L 121.025153 224.64 
L 120.702483 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.025153 224.64 
L 121.025153 496.44 
L 121.122088 496.44 
L 121.122088 224.64 
L 121.025153 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.122088 224.64 
L 121.122088 496.44 
L 121.495321 496.44 
L 121.495321 224.64 
L 121.122088 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 121.495321 224.64 
L 121.495321 496.44 
L 122.442954 496.44 
L 122.442954 224.64 
L 121.495321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.442954 224.64 
L 122.442954 496.44 
L 122.528317 496.44 
L 122.528317 224.64 
L 122.442954 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.528736 224.64 
L 122.528736 496.44 
L 122.839834 496.44 
L 122.839834 224.64 
L 122.528736 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 122.839834 224.64 
L 122.839834 496.44 
L 123.179442 496.44 
L 123.179442 224.64 
L 122.839834 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.179442 224.64 
L 123.179442 496.44 
L 123.512342 496.44 
L 123.512342 224.64 
L 123.179442 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.512342 224.64 
L 123.512342 496.44 
L 123.835599 496.44 
L 123.835599 224.64 
L 123.512342 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 123.835599 224.64 
L 123.835599 496.44 
L 124.254617 496.44 
L 124.254617 224.64 
L 123.835599 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 124.255036 224.64 
L 124.255036 496.44 
L 125.596111 496.44 
L 125.596111 224.64 
L 124.255036 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.596111 224.64 
L 125.596111 496.44 
L 125.760967 496.44 
L 125.760967 224.64 
L 125.596111 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.760967 224.64 
L 125.760967 496.44 
L 125.881885 496.44 
L 125.881885 224.64 
L 125.760967 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 125.881885 224.64 
L 125.881885 496.44 
L 126.188287 496.44 
L 126.188287 224.64 
L 125.881885 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.188287 224.64 
L 126.188287 496.44 
L 126.363206 496.44 
L 126.363206 224.64 
L 126.188287 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 126.363206 224.64 
L 126.363206 496.44 
L 127.612712 496.44 
L 127.612712 224.64 
L 126.363206 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.612712 224.64 
L 127.612712 496.44 
L 127.711408 496.44 
L 127.711408 224.64 
L 127.612712 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.711828 224.64 
L 127.711828 496.44 
L 127.992151 496.44 
L 127.992151 224.64 
L 127.711828 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 127.992151 224.64 
L 127.992151 496.44 
L 128.076257 496.44 
L 128.076257 224.64 
L 127.992151 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.076676 224.64 
L 128.076676 496.44 
L 128.096717 496.44 
L 128.096717 224.64 
L 128.076676 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.096717 224.64 
L 128.096717 496.44 
L 128.601182 496.44 
L 128.601182 224.64 
L 128.096717 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.601182 224.64 
L 128.601182 496.44 
L 128.844442 496.44 
L 128.844442 224.64 
L 128.601182 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.844442 224.64 
L 128.844442 496.44 
L 128.85811 496.44 
L 128.85811 224.64 
L 128.844442 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.85811 224.64 
L 128.85811 496.44 
L 128.868927 496.44 
L 128.868927 224.64 
L 128.85811 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 128.881841 224.64 
L 128.881841 496.44 
L 129.05349 496.44 
L 129.05349 224.64 
L 128.881841 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.05349 224.64 
L 129.05349 496.44 
L 129.502695 496.44 
L 129.502695 224.64 
L 129.05349 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.503282 224.64 
L 129.503282 496.44 
L 129.724908 496.44 
L 129.724908 224.64 
L 129.503282 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 129.724908 224.64 
L 129.724908 496.44 
L 130.027788 496.44 
L 130.027788 224.64 
L 129.724908 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.027788 224.64 
L 130.027788 496.44 
L 130.162373 496.44 
L 130.162373 224.64 
L 130.027788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.162373 224.64 
L 130.162373 496.44 
L 130.340982 496.44 
L 130.340982 224.64 
L 130.162373 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.340982 224.64 
L 130.340982 496.44 
L 130.798824 496.44 
L 130.798824 224.64 
L 130.340982 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.798824 224.64 
L 130.798824 496.44 
L 130.909763 496.44 
L 130.909763 224.64 
L 130.798824 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.909763 224.64 
L 130.909763 496.44 
L 130.948922 496.44 
L 130.948922 224.64 
L 130.909763 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.948922 224.64 
L 130.948922 496.44 
L 130.962842 496.44 
L 130.962842 224.64 
L 130.948922 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 130.97106 224.64 
L 130.97106 496.44 
L 132.741425 496.44 
L 132.741425 224.64 
L 130.97106 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 132.741425 224.64 
L 132.741425 496.44 
L 134.525374 496.44 
L 134.525374 224.64 
L 132.741425 224.64 
z
" style="fill:#f9f9fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.525374 224.64 
L 134.525374 496.44 
L 134.539293 496.44 
L 134.539293 224.64 
L 134.525374 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.539293 224.64 
L 134.539293 496.44 
L 134.568894 496.44 
L 134.568894 224.64 
L 134.539293 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.573422 224.64 
L 134.573422 496.44 
L 134.646375 496.44 
L 134.646375 224.64 
L 134.573422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.646375 224.64 
L 134.646375 496.44 
L 134.667841 496.44 
L 134.667841 224.64 
L 134.646375 224.64 
z
" style="fill:#e9e9f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.667841 224.64 
L 134.667841 496.44 
L 134.692914 496.44 
L 134.692914 224.64 
L 134.667841 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.692914 224.64 
L 134.692914 496.44 
L 134.73308 496.44 
L 134.73308 224.64 
L 134.692914 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.733499 224.64 
L 134.733499 496.44 
L 134.78574 496.44 
L 134.78574 224.64 
L 134.733499 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.788675 224.64 
L 134.788675 496.44 
L 134.811148 496.44 
L 134.811148 224.64 
L 134.788675 224.64 
z
" style="fill:#eecaca;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.819365 224.64 
L 134.819365 496.44 
L 134.981036 496.44 
L 134.981036 224.64 
L 134.819365 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 134.981036 224.64 
L 134.981036 496.44 
L 135.059271 496.44 
L 135.059271 224.64 
L 134.981036 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.059271 224.64 
L 135.059271 496.44 
L 135.102037 496.44 
L 135.102037 224.64 
L 135.059271 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.102708 224.64 
L 135.102708 496.44 
L 135.125264 496.44 
L 135.125264 224.64 
L 135.102708 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.127444 224.64 
L 135.127444 496.44 
L 135.148408 496.44 
L 135.148408 224.64 
L 135.127444 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.148827 224.64 
L 135.148827 496.44 
L 135.326597 496.44 
L 135.326597 224.64 
L 135.148827 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.336744 224.64 
L 135.336744 496.44 
L 135.352928 496.44 
L 135.352928 224.64 
L 135.336744 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.354018 224.64 
L 135.354018 496.44 
L 135.364164 496.44 
L 135.364164 224.64 
L 135.354018 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.364583 224.64 
L 135.364583 496.44 
L 135.464537 496.44 
L 135.464537 224.64 
L 135.364583 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.464537 224.64 
L 135.464537 496.44 
L 135.477954 496.44 
L 135.477954 224.64 
L 135.464537 224.64 
z
" style="fill:#f0d1d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.478624 224.64 
L 135.478624 496.44 
L 135.548139 496.44 
L 135.548139 224.64 
L 135.478624 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.564155 224.64 
L 135.564155 496.44 
L 135.680545 496.44 
L 135.680545 224.64 
L 135.564155 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.689936 224.64 
L 135.689936 496.44 
L 135.699579 496.44 
L 135.699579 224.64 
L 135.689936 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.699579 224.64 
L 135.699579 496.44 
L 135.723478 496.44 
L 135.723478 224.64 
L 135.699579 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 135.731779 224.64 
L 135.731779 496.44 
L 136.122958 496.44 
L 136.122958 224.64 
L 135.731779 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.122958 224.64 
L 136.122958 496.44 
L 136.278926 496.44 
L 136.278926 224.64 
L 136.122958 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.278926 224.64 
L 136.278926 496.44 
L 136.497701 496.44 
L 136.497701 224.64 
L 136.278926 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.497701 224.64 
L 136.497701 496.44 
L 136.574259 496.44 
L 136.574259 224.64 
L 136.497701 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.574259 224.64 
L 136.574259 496.44 
L 136.962167 496.44 
L 136.962167 224.64 
L 136.574259 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 136.962167 224.64 
L 136.962167 496.44 
L 137.158301 496.44 
L 137.158301 224.64 
L 136.962167 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.158301 224.64 
L 137.158301 496.44 
L 137.833325 496.44 
L 137.833325 224.64 
L 137.158301 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 137.833325 224.64 
L 137.833325 496.44 
L 138.17134 496.44 
L 138.17134 224.64 
L 137.833325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.17134 224.64 
L 138.17134 496.44 
L 138.574006 496.44 
L 138.574006 224.64 
L 138.17134 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.574006 224.64 
L 138.574006 496.44 
L 138.790014 496.44 
L 138.790014 224.64 
L 138.574006 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.790014 224.64 
L 138.790014 496.44 
L 138.979691 496.44 
L 138.979691 224.64 
L 138.790014 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 138.979691 224.64 
L 138.979691 496.44 
L 139.101866 496.44 
L 139.101866 224.64 
L 138.979691 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 139.101866 224.64 
L 139.101866 496.44 
L 140.274563 496.44 
L 140.274563 224.64 
L 139.101866 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.274563 224.64 
L 140.274563 496.44 
L 140.584235 496.44 
L 140.584235 224.64 
L 140.274563 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.584235 224.64 
L 140.584235 496.44 
L 140.789677 496.44 
L 140.789677 224.64 
L 140.584235 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 140.789677 224.64 
L 140.789677 496.44 
L 141.260013 496.44 
L 141.260013 224.64 
L 140.789677 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.260013 224.64 
L 141.260013 496.44 
L 141.57958 496.44 
L 141.57958 224.64 
L 141.260013 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 141.57958 224.64 
L 141.57958 496.44 
L 143.602387 496.44 
L 143.602387 224.64 
L 141.57958 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.602387 224.64 
L 143.602387 496.44 
L 143.788124 496.44 
L 143.788124 224.64 
L 143.602387 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 143.788124 224.64 
L 143.788124 496.44 
L 144.009582 496.44 
L 144.009582 224.64 
L 143.788124 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.009582 224.64 
L 144.009582 496.44 
L 144.506751 496.44 
L 144.506751 224.64 
L 144.009582 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.506751 224.64 
L 144.506751 496.44 
L 144.726532 496.44 
L 144.726532 224.64 
L 144.506751 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.726532 224.64 
L 144.726532 496.44 
L 144.826738 496.44 
L 144.826738 224.64 
L 144.726532 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.826738 224.64 
L 144.826738 496.44 
L 144.993607 496.44 
L 144.993607 224.64 
L 144.826738 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 144.993607 224.64 
L 144.993607 496.44 
L 145.107313 496.44 
L 145.107313 224.64 
L 144.993607 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.107313 224.64 
L 145.107313 496.44 
L 145.436187 496.44 
L 145.436187 224.64 
L 145.107313 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.437026 224.64 
L 145.437026 496.44 
L 145.532703 496.44 
L 145.532703 224.64 
L 145.437026 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.532703 224.64 
L 145.532703 496.44 
L 145.860236 496.44 
L 145.860236 224.64 
L 145.532703 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 145.860236 224.64 
L 145.860236 496.44 
L 146.067188 496.44 
L 146.067188 224.64 
L 145.860236 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.067188 224.64 
L 146.067188 496.44 
L 146.358999 496.44 
L 146.358999 224.64 
L 146.067188 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.358999 224.64 
L 146.358999 496.44 
L 146.657351 496.44 
L 146.657351 224.64 
L 146.358999 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 146.657351 224.64 
L 146.657351 496.44 
L 147.193261 496.44 
L 147.193261 224.64 
L 146.657351 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.1941 224.64 
L 147.1941 496.44 
L 147.455976 496.44 
L 147.455976 224.64 
L 147.1941 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.455976 224.64 
L 147.455976 496.44 
L 147.608254 496.44 
L 147.608254 224.64 
L 147.455976 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.608254 224.64 
L 147.608254 496.44 
L 147.83424 496.44 
L 147.83424 224.64 
L 147.608254 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 147.83424 224.64 
L 147.83424 496.44 
L 148.124123 496.44 
L 148.124123 224.64 
L 147.83424 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.124542 224.64 
L 148.124542 496.44 
L 148.424907 496.44 
L 148.424907 224.64 
L 148.124542 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.424907 224.64 
L 148.424907 496.44 
L 148.728877 496.44 
L 148.728877 224.64 
L 148.424907 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.728877 224.64 
L 148.728877 496.44 
L 148.78028 496.44 
L 148.78028 224.64 
L 148.728877 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.78028 224.64 
L 148.78028 496.44 
L 148.969957 496.44 
L 148.969957 224.64 
L 148.78028 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 148.970796 224.64 
L 148.970796 496.44 
L 149.061358 496.44 
L 149.061358 224.64 
L 148.970796 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.061358 224.64 
L 149.061358 496.44 
L 149.764137 496.44 
L 149.764137 224.64 
L 149.061358 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.764137 224.64 
L 149.764137 496.44 
L 149.898052 496.44 
L 149.898052 224.64 
L 149.764137 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.898052 224.64 
L 149.898052 496.44 
L 149.977545 496.44 
L 149.977545 224.64 
L 149.898052 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 149.977545 224.64 
L 149.977545 496.44 
L 150.043874 496.44 
L 150.043874 224.64 
L 149.977545 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.043874 224.64 
L 150.043874 496.44 
L 150.247722 496.44 
L 150.247722 224.64 
L 150.043874 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 150.247722 224.64 
L 150.247722 496.44 
L 151.445407 496.44 
L 151.445407 224.64 
L 150.247722 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.445407 224.64 
L 151.445407 496.44 
L 151.69873 496.44 
L 151.69873 224.64 
L 151.445407 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 151.69873 224.64 
L 151.69873 496.44 
L 152.011253 496.44 
L 152.011253 224.64 
L 151.69873 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.011253 224.64 
L 152.011253 496.44 
L 152.168814 496.44 
L 152.168814 224.64 
L 152.011253 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.169234 224.64 
L 152.169234 496.44 
L 152.401802 496.44 
L 152.401802 224.64 
L 152.169234 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_94">
    <path clip-path="url(#p9901fb19d8)" d="M 152.403522 224.64 
L 152.403522 496.44 
L 152.606155 496.44 
L 152.606155 224.64 
L 152.403522 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.606574 224.64 
L 152.606574 496.44 
L 152.849499 496.44 
L 152.849499 224.64 
L 152.606574 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 152.849499 224.64 
L 152.849499 496.44 
L 153.125462 496.44 
L 153.125462 224.64 
L 152.849499 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.125881 224.64 
L 153.125881 496.44 
L 153.204033 496.44 
L 153.204033 224.64 
L 153.125881 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.20462 224.64 
L 153.20462 496.44 
L 153.80342 496.44 
L 153.80342 224.64 
L 153.20462 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.80342 224.64 
L 153.80342 496.44 
L 153.938006 496.44 
L 153.938006 224.64 
L 153.80342 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 153.938006 224.64 
L 153.938006 496.44 
L 154.129109 496.44 
L 154.129109 224.64 
L 153.938006 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.129109 224.64 
L 154.129109 496.44 
L 154.17657 496.44 
L 154.17657 224.64 
L 154.129109 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.17657 224.64 
L 154.17657 496.44 
L 154.486158 496.44 
L 154.486158 224.64 
L 154.17657 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.486158 224.64 
L 154.486158 496.44 
L 154.569593 496.44 
L 154.569593 224.64 
L 154.486158 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.569593 224.64 
L 154.569593 496.44 
L 154.84782 496.44 
L 154.84782 224.64 
L 154.569593 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 154.84782 224.64 
L 154.84782 496.44 
L 155.012844 496.44 
L 155.012844 224.64 
L 154.84782 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.012844 224.64 
L 155.012844 496.44 
L 155.151958 496.44 
L 155.151958 224.64 
L 155.012844 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.151958 224.64 
L 155.151958 496.44 
L 155.300212 496.44 
L 155.300212 224.64 
L 155.151958 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.300212 224.64 
L 155.300212 496.44 
L 155.500287 496.44 
L 155.500287 224.64 
L 155.300212 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.50079 224.64 
L 155.50079 496.44 
L 155.608039 496.44 
L 155.608039 224.64 
L 155.50079 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.608039 224.64 
L 155.608039 496.44 
L 155.908152 496.44 
L 155.908152 224.64 
L 155.608039 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 155.908152 224.64 
L 155.908152 496.44 
L 156.274091 496.44 
L 156.274091 224.64 
L 155.908152 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.274091 224.64 
L 156.274091 496.44 
L 156.46511 496.44 
L 156.46511 224.64 
L 156.274091 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.46511 224.64 
L 156.46511 496.44 
L 156.831719 496.44 
L 156.831719 224.64 
L 156.46511 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 156.831719 224.64 
L 156.831719 496.44 
L 157.252162 496.44 
L 157.252162 224.64 
L 156.831719 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.252162 224.64 
L 157.252162 496.44 
L 157.494667 496.44 
L 157.494667 224.64 
L 157.252162 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.494667 224.64 
L 157.494667 496.44 
L 157.656757 496.44 
L 157.656757 224.64 
L 157.494667 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.656757 224.64 
L 157.656757 496.44 
L 157.904881 496.44 
L 157.904881 224.64 
L 157.656757 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 157.904881 224.64 
L 157.904881 496.44 
L 158.146799 496.44 
L 158.146799 224.64 
L 157.904881 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.146799 224.64 
L 158.146799 496.44 
L 158.685476 496.44 
L 158.685476 224.64 
L 158.146799 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.685476 224.64 
L 158.685476 496.44 
L 158.861989 496.44 
L 158.861989 224.64 
L 158.685476 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 158.861989 224.64 
L 158.861989 496.44 
L 159.159334 496.44 
L 159.159334 224.64 
L 158.861989 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.159334 224.64 
L 159.159334 496.44 
L 159.548165 496.44 
L 159.548165 224.64 
L 159.159334 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.548165 224.64 
L 159.548165 496.44 
L 159.591098 496.44 
L 159.591098 224.64 
L 159.548165 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.591098 224.64 
L 159.591098 496.44 
L 159.744383 496.44 
L 159.744383 224.64 
L 159.591098 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 159.744383 224.64 
L 159.744383 496.44 
L 160.067639 496.44 
L 160.067639 224.64 
L 159.744383 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.067639 224.64 
L 160.067639 496.44 
L 160.364566 496.44 
L 160.364566 224.64 
L 160.067639 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.364566 224.64 
L 160.364566 496.44 
L 160.873727 496.44 
L 160.873727 224.64 
L 160.364566 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 160.873727 224.64 
L 160.873727 496.44 
L 161.432948 496.44 
L 161.432948 224.64 
L 160.873727 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.432948 224.64 
L 161.432948 496.44 
L 161.568456 496.44 
L 161.568456 224.64 
L 161.432948 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.568456 224.64 
L 161.568456 496.44 
L 161.701029 496.44 
L 161.701029 224.64 
L 161.568456 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 161.701029 224.64 
L 161.701029 496.44 
L 162.031246 496.44 
L 162.031246 224.64 
L 161.701029 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.031665 224.64 
L 162.031665 496.44 
L 162.231908 496.44 
L 162.231908 224.64 
L 162.031665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.231908 224.64 
L 162.231908 496.44 
L 162.537639 496.44 
L 162.537639 224.64 
L 162.231908 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.537639 224.64 
L 162.537639 496.44 
L 162.74241 496.44 
L 162.74241 224.64 
L 162.537639 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.74241 224.64 
L 162.74241 496.44 
L 162.849575 496.44 
L 162.849575 224.64 
L 162.74241 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 162.849575 224.64 
L 162.849575 496.44 
L 163.191531 496.44 
L 163.191531 224.64 
L 162.849575 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.191531 224.64 
L 163.191531 496.44 
L 163.342133 496.44 
L 163.342133 224.64 
L 163.191531 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.342133 224.64 
L 163.342133 496.44 
L 163.699351 496.44 
L 163.699351 224.64 
L 163.342133 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.699351 224.64 
L 163.699351 496.44 
L 163.888609 496.44 
L 163.888609 224.64 
L 163.699351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.888609 224.64 
L 163.888609 496.44 
L 163.930703 496.44 
L 163.930703 224.64 
L 163.888609 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 163.931123 224.64 
L 163.931123 496.44 
L 164.057574 496.44 
L 164.057574 224.64 
L 163.931123 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.057574 224.64 
L 164.057574 496.44 
L 164.472315 496.44 
L 164.472315 224.64 
L 164.057574 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.472315 224.64 
L 164.472315 496.44 
L 164.668534 496.44 
L 164.668534 224.64 
L 164.472315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 164.668534 224.64 
L 164.668534 496.44 
L 165.035143 496.44 
L 165.035143 224.64 
L 164.668534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.035143 224.64 
L 165.035143 496.44 
L 165.203353 496.44 
L 165.203353 224.64 
L 165.035143 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.203353 224.64 
L 165.203353 496.44 
L 165.5921 496.44 
L 165.5921 224.64 
L 165.203353 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.5921 224.64 
L 165.5921 496.44 
L 165.97548 496.44 
L 165.97548 224.64 
L 165.5921 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 165.97548 224.64 
L 165.97548 496.44 
L 166.806891 496.44 
L 166.806891 224.64 
L 165.97548 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 166.806891 224.64 
L 166.806891 496.44 
L 167.055685 496.44 
L 167.055685 224.64 
L 166.806891 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.057027 224.64 
L 167.057027 496.44 
L 167.114299 496.44 
L 167.114299 224.64 
L 167.057027 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.114802 224.64 
L 167.114802 496.44 
L 167.197818 496.44 
L 167.197818 224.64 
L 167.114802 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.197818 224.64 
L 167.197818 496.44 
L 167.467156 496.44 
L 167.467156 224.64 
L 167.197818 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.467156 224.64 
L 167.467156 496.44 
L 167.476548 496.44 
L 167.476548 224.64 
L 167.467156 224.64 
z
" style="fill:#f5f5fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.476548 224.64 
L 167.476548 496.44 
L 167.540361 496.44 
L 167.540361 224.64 
L 167.476548 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.540361 224.64 
L 167.540361 496.44 
L 167.553652 496.44 
L 167.553652 224.64 
L 167.540361 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.563001 224.64 
L 167.563001 496.44 
L 167.577173 496.44 
L 167.577173 224.64 
L 167.563001 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.585977 224.64 
L 167.585977 496.44 
L 167.763664 496.44 
L 167.763664 224.64 
L 167.585977 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.767772 224.64 
L 167.767772 496.44 
L 167.782279 496.44 
L 167.782279 224.64 
L 167.767772 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.782698 224.64 
L 167.782698 496.44 
L 167.830411 496.44 
L 167.830411 224.64 
L 167.782698 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.835275 224.64 
L 167.835275 496.44 
L 167.864288 496.44 
L 167.864288 224.64 
L 167.835275 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 167.876363 224.64 
L 167.876363 496.44 
L 168.137191 496.44 
L 168.137191 224.64 
L 167.876363 224.64 
z
" style="fill:#f0f0f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.137191 224.64 
L 168.137191 496.44 
L 168.518768 496.44 
L 168.518768 224.64 
L 168.137191 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.526315 224.64 
L 168.526315 496.44 
L 168.545852 496.44 
L 168.545852 224.64 
L 168.526315 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.552812 224.64 
L 168.552812 496.44 
L 168.618302 496.44 
L 168.618302 224.64 
L 168.552812 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.623166 224.64 
L 168.623166 496.44 
L 168.832297 496.44 
L 168.832297 224.64 
L 168.623166 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.832297 224.64 
L 168.832297 496.44 
L 168.847391 496.44 
L 168.847391 224.64 
L 168.832297 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.8515 224.64 
L 168.8515 496.44 
L 168.862233 496.44 
L 168.862233 224.64 
L 168.8515 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 168.862652 224.64 
L 168.862652 496.44 
L 169.060212 496.44 
L 169.060212 224.64 
L 168.862652 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.060212 224.64 
L 169.060212 496.44 
L 169.28276 496.44 
L 169.28276 224.64 
L 169.060212 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.28276 224.64 
L 169.28276 496.44 
L 169.424306 496.44 
L 169.424306 224.64 
L 169.28276 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.424306 224.64 
L 169.424306 496.44 
L 169.576417 496.44 
L 169.576417 224.64 
L 169.424306 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.576417 224.64 
L 169.576417 496.44 
L 169.706809 496.44 
L 169.706809 224.64 
L 169.576417 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.707229 224.64 
L 169.707229 496.44 
L 169.986965 496.44 
L 169.986965 224.64 
L 169.707229 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 169.986965 224.64 
L 169.986965 496.44 
L 170.208507 496.44 
L 170.208507 224.64 
L 169.986965 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.208507 224.64 
L 170.208507 496.44 
L 170.318523 496.44 
L 170.318523 224.64 
L 170.208507 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.318523 224.64 
L 170.318523 496.44 
L 170.895941 496.44 
L 170.895941 224.64 
L 170.318523 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.895941 224.64 
L 170.895941 496.44 
L 170.939629 496.44 
L 170.939629 224.64 
L 170.895941 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.939629 224.64 
L 170.939629 496.44 
L 170.966294 496.44 
L 170.966294 224.64 
L 170.939629 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 170.967888 224.64 
L 170.967888 496.44 
L 171.016774 496.44 
L 171.016774 224.64 
L 170.967888 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.021303 224.64 
L 171.021303 496.44 
L 171.051574 496.44 
L 171.051574 224.64 
L 171.021303 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.051993 224.64 
L 171.051993 496.44 
L 171.075472 496.44 
L 171.075472 224.64 
L 171.051993 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.075472 224.64 
L 171.075472 496.44 
L 171.192951 496.44 
L 171.192951 224.64 
L 171.075472 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.192951 224.64 
L 171.192951 496.44 
L 171.24905 496.44 
L 171.24905 224.64 
L 171.192951 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.24905 224.64 
L 171.24905 496.44 
L 171.450047 496.44 
L 171.450047 224.64 
L 171.24905 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.450047 224.64 
L 171.450047 496.44 
L 171.583543 496.44 
L 171.583543 224.64 
L 171.450047 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 171.583543 224.64 
L 171.583543 496.44 
L 172.15769 496.44 
L 172.15769 224.64 
L 171.583543 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.158109 224.64 
L 172.158109 496.44 
L 172.36917 496.44 
L 172.36917 224.64 
L 172.158109 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 172.369673 224.64 
L 172.369673 496.44 
L 173.134085 496.44 
L 173.134085 224.64 
L 172.369673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.134085 224.64 
L 173.134085 496.44 
L 173.641904 496.44 
L 173.641904 224.64 
L 173.134085 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.642742 224.64 
L 173.642742 496.44 
L 173.896903 496.44 
L 173.896903 224.64 
L 173.642742 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.896903 224.64 
L 173.896903 496.44 
L 173.953756 496.44 
L 173.953756 224.64 
L 173.896903 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 173.953756 224.64 
L 173.953756 496.44 
L 174.332524 496.44 
L 174.332524 224.64 
L 173.953756 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.332524 224.64 
L 174.332524 496.44 
L 174.418642 496.44 
L 174.418642 224.64 
L 174.332524 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.422248 224.64 
L 174.422248 496.44 
L 174.569663 496.44 
L 174.569663 224.64 
L 174.422248 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 174.569663 224.64 
L 174.569663 496.44 
L 175.023815 496.44 
L 175.023815 224.64 
L 174.569663 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.023815 224.64 
L 175.023815 496.44 
L 175.082932 496.44 
L 175.082932 224.64 
L 175.023815 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.082932 224.64 
L 175.082932 496.44 
L 175.321077 496.44 
L 175.321077 224.64 
L 175.082932 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.321077 224.64 
L 175.321077 496.44 
L 175.397636 496.44 
L 175.397636 224.64 
L 175.321077 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.397636 224.64 
L 175.397636 496.44 
L 175.668735 496.44 
L 175.668735 224.64 
L 175.397636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 175.669155 224.64 
L 175.669155 496.44 
L 176.741646 496.44 
L 176.741646 224.64 
L 175.669155 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.741646 224.64 
L 176.741646 496.44 
L 176.80462 496.44 
L 176.80462 224.64 
L 176.741646 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 176.80462 224.64 
L 176.80462 496.44 
L 178.503248 496.44 
L 178.503248 224.64 
L 176.80462 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 178.503248 224.64 
L 178.503248 496.44 
L 179.009725 496.44 
L 179.009725 224.64 
L 178.503248 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.009725 224.64 
L 179.009725 496.44 
L 179.258184 496.44 
L 179.258184 224.64 
L 179.009725 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 179.258184 224.64 
L 179.258184 496.44 
L 180.089511 496.44 
L 180.089511 224.64 
L 179.258184 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.089511 224.64 
L 180.089511 496.44 
L 180.609741 496.44 
L 180.609741 224.64 
L 180.089511 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.609741 224.64 
L 180.609741 496.44 
L 180.863399 496.44 
L 180.863399 224.64 
L 180.609741 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.863399 224.64 
L 180.863399 496.44 
L 180.929895 496.44 
L 180.929895 224.64 
L 180.863399 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.930566 224.64 
L 180.930566 496.44 
L 180.96612 496.44 
L 180.96612 224.64 
L 180.930566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 180.966539 224.64 
L 180.966539 496.44 
L 181.019618 496.44 
L 181.019618 224.64 
L 180.966539 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.020038 224.64 
L 181.020038 496.44 
L 181.334741 496.44 
L 181.334741 224.64 
L 181.020038 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.334741 224.64 
L 181.334741 496.44 
L 181.690533 496.44 
L 181.690533 224.64 
L 181.334741 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.690953 224.64 
L 181.690953 496.44 
L 181.971779 496.44 
L 181.971779 224.64 
L 181.690953 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 181.971779 224.64 
L 181.971779 496.44 
L 182.214452 496.44 
L 182.214452 224.64 
L 181.971779 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.214452 224.64 
L 182.214452 496.44 
L 182.559343 496.44 
L 182.559343 224.64 
L 182.214452 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.559343 224.64 
L 182.559343 496.44 
L 182.647138 496.44 
L 182.647138 224.64 
L 182.559343 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.647138 224.64 
L 182.647138 496.44 
L 182.994712 496.44 
L 182.994712 224.64 
L 182.647138 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 182.994712 224.64 
L 182.994712 496.44 
L 183.319478 496.44 
L 183.319478 224.64 
L 182.994712 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.319478 224.64 
L 183.319478 496.44 
L 183.814384 496.44 
L 183.814384 224.64 
L 183.319478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.814384 224.64 
L 183.814384 496.44 
L 183.911068 496.44 
L 183.911068 224.64 
L 183.814384 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 183.911068 224.64 
L 183.911068 496.44 
L 184.505591 496.44 
L 184.505591 224.64 
L 183.911068 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 184.505591 224.64 
L 184.505591 496.44 
L 185.277382 496.44 
L 185.277382 224.64 
L 184.505591 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.277382 224.64 
L 185.277382 496.44 
L 185.388321 496.44 
L 185.388321 224.64 
L 185.277382 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.388321 224.64 
L 185.388321 496.44 
L 185.984858 496.44 
L 185.984858 224.64 
L 185.388321 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 185.984858 224.64 
L 185.984858 496.44 
L 186.128499 496.44 
L 186.128499 224.64 
L 185.984858 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.128499 224.64 
L 186.128499 496.44 
L 186.451337 496.44 
L 186.451337 224.64 
L 186.128499 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.451337 224.64 
L 186.451337 496.44 
L 186.637576 496.44 
L 186.637576 224.64 
L 186.451337 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.637576 224.64 
L 186.637576 496.44 
L 186.789184 496.44 
L 186.789184 224.64 
L 186.637576 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 186.789184 224.64 
L 186.789184 496.44 
L 187.250548 496.44 
L 187.250548 224.64 
L 186.789184 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.250548 224.64 
L 187.250548 496.44 
L 187.345806 496.44 
L 187.345806 224.64 
L 187.250548 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 187.345806 224.64 
L 187.345806 496.44 
L 188.159524 496.44 
L 188.159524 224.64 
L 187.345806 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.159524 224.64 
L 188.159524 496.44 
L 188.334778 496.44 
L 188.334778 224.64 
L 188.159524 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.334778 224.64 
L 188.334778 496.44 
L 188.618288 496.44 
L 188.618288 224.64 
L 188.334778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 188.618288 224.64 
L 188.618288 496.44 
L 189.077137 496.44 
L 189.077137 224.64 
L 188.618288 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.077137 224.64 
L 189.077137 496.44 
L 189.373225 496.44 
L 189.373225 224.64 
L 189.077137 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 189.373225 224.64 
L 189.373225 496.44 
L 190.05613 496.44 
L 190.05613 224.64 
L 189.373225 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.05613 224.64 
L 190.05613 496.44 
L 190.102166 496.44 
L 190.102166 224.64 
L 190.05613 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.102166 224.64 
L 190.102166 496.44 
L 190.527473 496.44 
L 190.527473 224.64 
L 190.102166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 190.527892 224.64 
L 190.527892 496.44 
L 191.140193 496.44 
L 191.140193 224.64 
L 190.527892 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.140193 224.64 
L 191.140193 496.44 
L 191.356788 496.44 
L 191.356788 224.64 
L 191.140193 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.356788 224.64 
L 191.356788 496.44 
L 191.80767 496.44 
L 191.80767 224.64 
L 191.356788 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.80767 224.64 
L 191.80767 496.44 
L 191.848088 496.44 
L 191.848088 224.64 
L 191.80767 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 191.848088 224.64 
L 191.848088 496.44 
L 192.046989 496.44 
L 192.046989 224.64 
L 191.848088 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.054117 224.64 
L 192.054117 496.44 
L 192.0703 496.44 
L 192.0703 224.64 
L 192.054117 224.64 
z
" style="fill:#c6c6ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.0703 224.64 
L 192.0703 496.44 
L 192.187528 496.44 
L 192.187528 224.64 
L 192.0703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.187528 224.64 
L 192.187528 496.44 
L 192.227359 496.44 
L 192.227359 224.64 
L 192.187528 224.64 
z
" style="fill:#4747cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.227359 224.64 
L 192.227359 496.44 
L 192.414604 496.44 
L 192.414604 224.64 
L 192.227359 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.414604 224.64 
L 192.414604 496.44 
L 192.667005 496.44 
L 192.667005 224.64 
L 192.414604 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.667005 224.64 
L 192.667005 496.44 
L 192.683608 496.44 
L 192.683608 224.64 
L 192.667005 224.64 
z
" style="fill:#f1f1f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.683608 224.64 
L 192.683608 496.44 
L 192.744485 496.44 
L 192.744485 224.64 
L 192.683608 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 192.744485 224.64 
L 192.744485 496.44 
L 193.08032 496.44 
L 193.08032 224.64 
L 192.744485 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.08032 224.64 
L 193.08032 496.44 
L 193.112185 496.44 
L 193.112185 224.64 
L 193.08032 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.112604 224.64 
L 193.112604 496.44 
L 193.186437 496.44 
L 193.186437 224.64 
L 193.112604 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_95">
    <path clip-path="url(#p9901fb19d8)" d="M 193.196542 224.64 
L 193.196542 496.44 
L 193.332679 496.44 
L 193.332679 224.64 
L 193.196542 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.332679 224.64 
L 193.332679 496.44 
L 193.479591 496.44 
L 193.479591 224.64 
L 193.332679 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.48001 224.64 
L 193.48001 496.44 
L 193.868505 496.44 
L 193.868505 224.64 
L 193.48001 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.868924 224.64 
L 193.868924 496.44 
L 193.945315 496.44 
L 193.945315 224.64 
L 193.868924 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 193.945315 224.64 
L 193.945315 496.44 
L 194.019023 496.44 
L 194.019023 224.64 
L 193.945315 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.019023 224.64 
L 194.019023 496.44 
L 194.410788 496.44 
L 194.410788 224.64 
L 194.019023 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.410788 224.64 
L 194.410788 496.44 
L 194.695556 496.44 
L 194.695556 224.64 
L 194.410788 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 194.695556 224.64 
L 194.695556 496.44 
L 195.14627 496.44 
L 195.14627 224.64 
L 194.695556 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.14627 224.64 
L 195.14627 496.44 
L 195.188533 496.44 
L 195.188533 224.64 
L 195.14627 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.188533 224.64 
L 195.188533 496.44 
L 195.339805 496.44 
L 195.339805 224.64 
L 195.188533 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.339805 224.64 
L 195.339805 496.44 
L 195.76637 496.44 
L 195.76637 224.64 
L 195.339805 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 195.76637 224.64 
L 195.76637 496.44 
L 196.15889 496.44 
L 196.15889 224.64 
L 195.76637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.15889 224.64 
L 196.15889 496.44 
L 196.563736 496.44 
L 196.563736 224.64 
L 196.15889 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.563736 224.64 
L 196.563736 496.44 
L 196.934454 496.44 
L 196.934454 224.64 
L 196.563736 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 196.934454 224.64 
L 196.934454 496.44 
L 197.237083 496.44 
L 197.237083 224.64 
L 196.934454 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.237083 224.64 
L 197.237083 496.44 
L 197.792111 496.44 
L 197.792111 224.64 
L 197.237083 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.792111 224.64 
L 197.792111 496.44 
L 197.871353 496.44 
L 197.871353 224.64 
L 197.792111 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 197.871353 224.64 
L 197.871353 496.44 
L 198.646331 496.44 
L 198.646331 224.64 
L 197.871353 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 198.646331 224.64 
L 198.646331 496.44 
L 199.480593 496.44 
L 199.480593 224.64 
L 198.646331 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.480593 224.64 
L 199.480593 496.44 
L 199.593125 496.44 
L 199.593125 224.64 
L 199.480593 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 199.593544 224.64 
L 199.593544 496.44 
L 200.11914 496.44 
L 200.11914 224.64 
L 199.593544 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.11914 224.64 
L 200.11914 496.44 
L 200.263369 496.44 
L 200.263369 224.64 
L 200.11914 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 200.263369 224.64 
L 200.263369 496.44 
L 201.093187 496.44 
L 201.093187 224.64 
L 200.263369 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.093187 224.64 
L 201.093187 496.44 
L 201.286721 496.44 
L 201.286721 224.64 
L 201.093187 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.286721 224.64 
L 201.286721 496.44 
L 201.359087 496.44 
L 201.359087 224.64 
L 201.286721 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.359087 224.64 
L 201.359087 496.44 
L 201.506167 496.44 
L 201.506167 224.64 
L 201.359087 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.506167 224.64 
L 201.506167 496.44 
L 201.529562 496.44 
L 201.529562 224.64 
L 201.506167 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.529562 224.64 
L 201.529562 496.44 
L 201.604108 496.44 
L 201.604108 224.64 
L 201.529562 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.604108 224.64 
L 201.604108 496.44 
L 201.687207 496.44 
L 201.687207 224.64 
L 201.604108 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.687207 224.64 
L 201.687207 496.44 
L 201.860785 496.44 
L 201.860785 224.64 
L 201.687207 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.860785 224.64 
L 201.860785 496.44 
L 201.998389 496.44 
L 201.998389 224.64 
L 201.860785 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 201.998389 224.64 
L 201.998389 496.44 
L 202.243578 496.44 
L 202.243578 224.64 
L 201.998389 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.243578 224.64 
L 202.243578 496.44 
L 202.70947 496.44 
L 202.70947 224.64 
L 202.243578 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 202.70947 224.64 
L 202.70947 496.44 
L 203.046227 496.44 
L 203.046227 224.64 
L 202.70947 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.046227 224.64 
L 203.046227 496.44 
L 203.373592 496.44 
L 203.373592 224.64 
L 203.046227 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.373592 224.64 
L 203.373592 496.44 
L 203.47841 496.44 
L 203.47841 224.64 
L 203.373592 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.47841 224.64 
L 203.47841 496.44 
L 203.835124 496.44 
L 203.835124 224.64 
L 203.47841 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 203.835124 224.64 
L 203.835124 496.44 
L 204.155781 496.44 
L 204.155781 224.64 
L 203.835124 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.155781 224.64 
L 204.155781 496.44 
L 204.280556 496.44 
L 204.280556 224.64 
L 204.155781 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 204.280556 224.64 
L 204.280556 496.44 
L 205.091423 496.44 
L 205.091423 224.64 
L 204.280556 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.091423 224.64 
L 205.091423 496.44 
L 205.191041 496.44 
L 205.191041 224.64 
L 205.091423 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.191041 224.64 
L 205.191041 496.44 
L 205.387427 496.44 
L 205.387427 224.64 
L 205.191041 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.387427 224.64 
L 205.387427 496.44 
L 205.877888 496.44 
L 205.877888 224.64 
L 205.387427 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 205.878307 224.64 
L 205.878307 496.44 
L 207.100226 496.44 
L 207.100226 224.64 
L 205.878307 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 207.100645 224.64 
L 207.100645 496.44 
L 208.325583 496.44 
L 208.325583 224.64 
L 207.100645 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.325583 224.64 
L 208.325583 496.44 
L 208.616346 496.44 
L 208.616346 224.64 
L 208.325583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.616346 224.64 
L 208.616346 496.44 
L 208.969832 496.44 
L 208.969832 224.64 
L 208.616346 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 208.969832 224.64 
L 208.969832 496.44 
L 209.343233 496.44 
L 209.343233 224.64 
L 208.969832 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 209.343652 224.64 
L 209.343652 496.44 
L 210.242482 496.44 
L 210.242482 224.64 
L 209.343652 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 210.242482 224.64 
L 210.242482 496.44 
L 211.001947 496.44 
L 211.001947 224.64 
L 210.242482 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.002366 224.64 
L 211.002366 496.44 
L 211.378367 496.44 
L 211.378367 224.64 
L 211.002366 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.378367 224.64 
L 211.378367 496.44 
L 211.50356 496.44 
L 211.50356 224.64 
L 211.378367 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 211.508005 224.64 
L 211.508005 496.44 
L 212.487669 496.44 
L 212.487669 224.64 
L 211.508005 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 212.487669 224.64 
L 212.487669 496.44 
L 213.189023 496.44 
L 213.189023 224.64 
L 212.487669 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.189023 224.64 
L 213.189023 496.44 
L 213.792268 496.44 
L 213.792268 224.64 
L 213.189023 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.792268 224.64 
L 213.792268 496.44 
L 213.91352 496.44 
L 213.91352 224.64 
L 213.792268 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 213.91352 224.64 
L 213.91352 496.44 
L 214.105043 496.44 
L 214.105043 224.64 
L 213.91352 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.105043 224.64 
L 214.105043 496.44 
L 214.208435 496.44 
L 214.208435 224.64 
L 214.105043 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 214.208435 224.64 
L 214.208435 496.44 
L 215.800316 496.44 
L 215.800316 224.64 
L 214.208435 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 215.800316 224.64 
L 215.800316 496.44 
L 216.795326 496.44 
L 216.795326 224.64 
L 215.800316 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.795326 224.64 
L 216.795326 496.44 
L 216.891926 496.44 
L 216.891926 224.64 
L 216.795326 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 216.891926 224.64 
L 216.891926 496.44 
L 217.205372 496.44 
L 217.205372 224.64 
L 216.891926 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.205372 224.64 
L 217.205372 496.44 
L 217.929534 496.44 
L 217.929534 224.64 
L 217.205372 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 217.929534 224.64 
L 217.929534 496.44 
L 218.310985 496.44 
L 218.310985 224.64 
L 217.929534 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.310985 224.64 
L 218.310985 496.44 
L 218.72799 496.44 
L 218.72799 224.64 
L 218.310985 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 218.72799 224.64 
L 218.72799 496.44 
L 219.071875 496.44 
L 219.071875 224.64 
L 218.72799 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.071875 224.64 
L 219.071875 496.44 
L 219.326958 496.44 
L 219.326958 224.64 
L 219.071875 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.326958 224.64 
L 219.326958 496.44 
L 219.602418 496.44 
L 219.602418 224.64 
L 219.326958 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 219.602418 224.64 
L 219.602418 496.44 
L 220.033092 496.44 
L 220.033092 224.64 
L 219.602418 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 220.033092 224.64 
L 220.033092 496.44 
L 221.223481 496.44 
L 221.223481 224.64 
L 220.033092 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.223481 224.64 
L 221.223481 496.44 
L 221.938 496.44 
L 221.938 224.64 
L 221.223481 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 221.938 224.64 
L 221.938 496.44 
L 222.897792 496.44 
L 222.897792 224.64 
L 221.938 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 222.897792 224.64 
L 222.897792 496.44 
L 223.002944 496.44 
L 223.002944 224.64 
L 222.897792 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.002944 224.64 
L 223.002944 496.44 
L 223.620444 496.44 
L 223.620444 224.64 
L 223.002944 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.620444 224.64 
L 223.620444 496.44 
L 223.652225 496.44 
L 223.652225 224.64 
L 223.620444 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 223.652225 224.64 
L 223.652225 496.44 
L 224.241131 496.44 
L 224.241131 224.64 
L 223.652225 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.24155 224.64 
L 224.24155 496.44 
L 224.31249 496.44 
L 224.31249 224.64 
L 224.24155 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.31249 224.64 
L 224.31249 496.44 
L 224.621072 496.44 
L 224.621072 224.64 
L 224.31249 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.621072 224.64 
L 224.621072 496.44 
L 224.789367 496.44 
L 224.789367 224.64 
L 224.621072 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 224.789367 224.64 
L 224.789367 496.44 
L 225.072374 496.44 
L 225.072374 224.64 
L 224.789367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.072374 224.64 
L 225.072374 496.44 
L 225.135264 496.44 
L 225.135264 224.64 
L 225.072374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.135264 224.64 
L 225.135264 496.44 
L 225.404519 496.44 
L 225.404519 224.64 
L 225.135264 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.404519 224.64 
L 225.404519 496.44 
L 225.788654 496.44 
L 225.788654 224.64 
L 225.404519 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.788654 224.64 
L 225.788654 496.44 
L 225.923071 496.44 
L 225.923071 224.64 
L 225.788654 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 225.92391 224.64 
L 225.92391 496.44 
L 226.020677 496.44 
L 226.020677 224.64 
L 225.92391 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.020677 224.64 
L 226.020677 496.44 
L 226.166918 496.44 
L 226.166918 224.64 
L 226.020677 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.166918 224.64 
L 226.166918 496.44 
L 226.296892 496.44 
L 226.296892 224.64 
L 226.166918 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.296892 224.64 
L 226.296892 496.44 
L 226.383345 496.44 
L 226.383345 224.64 
L 226.296892 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_96">
    <path clip-path="url(#p9901fb19d8)" d="M 226.385065 224.64 
L 226.385065 496.44 
L 226.394917 496.44 
L 226.394917 224.64 
L 226.385065 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 226.394917 224.64 
L 226.394917 496.44 
L 227.031955 496.44 
L 227.031955 224.64 
L 226.394917 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.031955 224.64 
L 227.031955 496.44 
L 227.158826 496.44 
L 227.158826 224.64 
L 227.031955 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.158826 224.64 
L 227.158826 496.44 
L 227.437976 496.44 
L 227.437976 224.64 
L 227.158826 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.437976 224.64 
L 227.437976 496.44 
L 227.829741 496.44 
L 227.829741 224.64 
L 227.437976 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.830328 224.64 
L 227.830328 496.44 
L 227.931959 496.44 
L 227.931959 224.64 
L 227.830328 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 227.932797 224.64 
L 227.932797 496.44 
L 228.025875 496.44 
L 228.025875 224.64 
L 227.932797 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.025875 224.64 
L 228.025875 496.44 
L 228.127422 496.44 
L 228.127422 224.64 
L 228.025875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.127422 224.64 
L 228.127422 496.44 
L 228.286996 496.44 
L 228.286996 224.64 
L 228.127422 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.286996 224.64 
L 228.286996 496.44 
L 228.858544 496.44 
L 228.858544 224.64 
L 228.286996 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 228.858544 224.64 
L 228.858544 496.44 
L 229.139874 496.44 
L 229.139874 224.64 
L 228.858544 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.139874 224.64 
L 229.139874 496.44 
L 229.345484 496.44 
L 229.345484 224.64 
L 229.139874 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.345484 224.64 
L 229.345484 496.44 
L 229.583461 496.44 
L 229.583461 224.64 
L 229.345484 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.58388 224.64 
L 229.58388 496.44 
L 229.834603 496.44 
L 229.834603 224.64 
L 229.58388 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 229.834603 224.64 
L 229.834603 496.44 
L 230.263683 496.44 
L 230.263683 224.64 
L 229.834603 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.263683 224.64 
L 230.263683 496.44 
L 230.661402 496.44 
L 230.661402 224.64 
L 230.263683 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.661402 224.64 
L 230.661402 496.44 
L 230.70073 496.44 
L 230.70073 224.64 
L 230.661402 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 230.70073 224.64 
L 230.70073 496.44 
L 231.719219 496.44 
L 231.719219 224.64 
L 230.70073 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 231.719806 224.64 
L 231.719806 496.44 
L 232.770075 496.44 
L 232.770075 224.64 
L 231.719806 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.770075 224.64 
L 232.770075 496.44 
L 232.978452 496.44 
L 232.978452 224.64 
L 232.770075 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 232.978452 224.64 
L 232.978452 496.44 
L 233.497508 496.44 
L 233.497508 224.64 
L 232.978452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.497508 224.64 
L 233.497508 496.44 
L 233.93447 496.44 
L 233.93447 224.64 
L 233.497508 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 233.93489 224.64 
L 233.93489 496.44 
L 234.188044 496.44 
L 234.188044 224.64 
L 233.93489 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.188044 224.64 
L 234.188044 496.44 
L 234.327577 496.44 
L 234.327577 224.64 
L 234.188044 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.327577 224.64 
L 234.327577 496.44 
L 234.552725 496.44 
L 234.552725 224.64 
L 234.327577 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.552725 224.64 
L 234.552725 496.44 
L 234.616538 496.44 
L 234.616538 224.64 
L 234.552725 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.616538 224.64 
L 234.616538 496.44 
L 234.627439 496.44 
L 234.627439 224.64 
L 234.616538 224.64 
z
" style="fill:#e2e2f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.627439 224.64 
L 234.627439 496.44 
L 234.683201 496.44 
L 234.683201 224.64 
L 234.627439 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.686723 224.64 
L 234.686723 496.44 
L 234.696953 496.44 
L 234.696953 224.64 
L 234.686723 224.64 
z
" style="fill:#d2d2f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.709783 224.64 
L 234.709783 496.44 
L 234.963315 496.44 
L 234.963315 224.64 
L 234.709783 224.64 
z
" style="fill:#b5b5e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 234.963315 224.64 
L 234.963315 496.44 
L 235.217183 496.44 
L 235.217183 224.64 
L 234.963315 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.217602 224.64 
L 235.217602 496.44 
L 235.359399 496.44 
L 235.359399 224.64 
L 235.217602 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.359399 224.64 
L 235.359399 496.44 
L 235.379356 496.44 
L 235.379356 224.64 
L 235.359399 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 235.379356 224.64 
L 235.379356 496.44 
L 236.223932 496.44 
L 236.223932 224.64 
L 235.379356 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 236.223932 224.64 
L 236.223932 496.44 
L 237.127877 496.44 
L 237.127877 224.64 
L 236.223932 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.128296 224.64 
L 237.128296 496.44 
L 237.966248 496.44 
L 237.966248 224.64 
L 237.128296 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 237.966667 224.64 
L 237.966667 496.44 
L 238.018489 496.44 
L 238.018489 224.64 
L 237.966667 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.018489 224.64 
L 238.018489 496.44 
L 238.341913 496.44 
L 238.341913 224.64 
L 238.018489 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.341913 224.64 
L 238.341913 496.44 
L 238.477841 496.44 
L 238.477841 224.64 
L 238.341913 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.477841 224.64 
L 238.477841 496.44 
L 238.850319 496.44 
L 238.850319 224.64 
L 238.477841 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.850319 224.64 
L 238.850319 496.44 
L 238.967799 496.44 
L 238.967799 224.64 
L 238.850319 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 238.967799 224.64 
L 238.967799 496.44 
L 239.040332 496.44 
L 239.040332 224.64 
L 238.967799 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.04159 224.64 
L 239.04159 496.44 
L 239.44325 496.44 
L 239.44325 224.64 
L 239.04159 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 239.44325 224.64 
L 239.44325 496.44 
L 240.094962 496.44 
L 240.094962 224.64 
L 239.44325 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.094962 224.64 
L 240.094962 496.44 
L 240.266276 496.44 
L 240.266276 224.64 
L 240.094962 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.266276 224.64 
L 240.266276 496.44 
L 240.99832 496.44 
L 240.99832 224.64 
L 240.266276 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 240.99832 224.64 
L 240.99832 496.44 
L 241.120411 496.44 
L 241.120411 224.64 
L 240.99832 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.120411 224.64 
L 241.120411 496.44 
L 241.435786 496.44 
L 241.435786 224.64 
L 241.120411 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.435786 224.64 
L 241.435786 496.44 
L 241.745039 496.44 
L 241.745039 224.64 
L 241.435786 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.745458 224.64 
L 241.745458 496.44 
L 241.778161 496.44 
L 241.778161 224.64 
L 241.745458 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 241.778161 224.64 
L 241.778161 496.44 
L 242.298726 496.44 
L 242.298726 224.64 
L 241.778161 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.298726 224.64 
L 242.298726 496.44 
L 242.602696 496.44 
L 242.602696 224.64 
L 242.298726 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.602696 224.64 
L 242.602696 496.44 
L 242.95874 496.44 
L 242.95874 224.64 
L 242.602696 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 242.95874 224.64 
L 242.95874 496.44 
L 243.187325 496.44 
L 243.187325 224.64 
L 242.95874 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.187325 224.64 
L 243.187325 496.44 
L 243.545549 496.44 
L 243.545549 224.64 
L 243.187325 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.545549 224.64 
L 243.545549 496.44 
L 243.72726 496.44 
L 243.72726 224.64 
L 243.545549 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.72726 224.64 
L 243.72726 496.44 
L 243.830401 496.44 
L 243.830401 224.64 
L 243.72726 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 243.83082 224.64 
L 243.83082 496.44 
L 244.228958 496.44 
L 244.228958 224.64 
L 243.83082 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.228958 224.64 
L 244.228958 496.44 
L 244.493601 496.44 
L 244.493601 224.64 
L 244.228958 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.493601 224.64 
L 244.493601 496.44 
L 244.732249 496.44 
L 244.732249 224.64 
L 244.493601 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.732249 224.64 
L 244.732249 496.44 
L 244.980876 496.44 
L 244.980876 224.64 
L 244.732249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 244.980876 224.64 
L 244.980876 496.44 
L 245.088292 496.44 
L 245.088292 224.64 
L 244.980876 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.088292 224.64 
L 245.088292 496.44 
L 245.417922 496.44 
L 245.417922 224.64 
L 245.088292 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.417922 224.64 
L 245.417922 496.44 
L 245.489701 496.44 
L 245.489701 224.64 
L 245.417922 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.489701 224.64 
L 245.489701 496.44 
L 245.8413 496.44 
L 245.8413 224.64 
L 245.489701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 245.8413 224.64 
L 245.8413 496.44 
L 246.239438 496.44 
L 246.239438 224.64 
L 245.8413 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.239438 224.64 
L 246.239438 496.44 
L 246.439765 496.44 
L 246.439765 224.64 
L 246.239438 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.439765 224.64 
L 246.439765 496.44 
L 246.737111 496.44 
L 246.737111 224.64 
L 246.439765 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 246.737111 224.64 
L 246.737111 496.44 
L 247.146486 496.44 
L 247.146486 224.64 
L 246.737111 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.146486 224.64 
L 247.146486 496.44 
L 247.297087 496.44 
L 247.297087 224.64 
L 247.146486 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.297087 224.64 
L 247.297087 496.44 
L 247.395532 496.44 
L 247.395532 224.64 
L 247.297087 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 247.395532 224.64 
L 247.395532 496.44 
L 248.146191 496.44 
L 248.146191 224.64 
L 247.395532 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.146191 224.64 
L 248.146191 496.44 
L 248.238011 496.44 
L 248.238011 224.64 
L 248.146191 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 248.238011 224.64 
L 248.238011 496.44 
L 249.839453 496.44 
L 249.839453 224.64 
L 248.238011 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.839453 224.64 
L 249.839453 496.44 
L 249.909303 496.44 
L 249.909303 224.64 
L 249.839453 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 249.909303 224.64 
L 249.909303 496.44 
L 250.132522 496.44 
L 250.132522 224.64 
L 249.909303 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.132522 224.64 
L 250.132522 496.44 
L 250.523784 496.44 
L 250.523784 224.64 
L 250.132522 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.523784 224.64 
L 250.523784 496.44 
L 250.812157 496.44 
L 250.812157 224.64 
L 250.523784 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 250.812157 224.64 
L 250.812157 496.44 
L 251.192267 496.44 
L 251.192267 224.64 
L 250.812157 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.192267 224.64 
L 251.192267 496.44 
L 251.302703 496.44 
L 251.302703 224.64 
L 251.192267 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.302703 224.64 
L 251.302703 496.44 
L 251.322073 496.44 
L 251.322073 224.64 
L 251.302703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.322492 224.64 
L 251.322492 496.44 
L 251.441313 496.44 
L 251.441313 224.64 
L 251.322492 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.441732 224.64 
L 251.441732 496.44 
L 251.689688 496.44 
L 251.689688 224.64 
L 251.441732 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.689688 224.64 
L 251.689688 496.44 
L 251.958691 496.44 
L 251.958691 224.64 
L 251.689688 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 251.958691 224.64 
L 251.958691 496.44 
L 252.335698 496.44 
L 252.335698 224.64 
L 251.958691 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.335698 224.64 
L 252.335698 496.44 
L 252.899364 496.44 
L 252.899364 224.64 
L 252.335698 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 252.899364 224.64 
L 252.899364 496.44 
L 254.163126 496.44 
L 254.163126 224.64 
L 252.899364 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.163126 224.64 
L 254.163126 496.44 
L 254.231718 496.44 
L 254.231718 224.64 
L 254.163126 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 254.231718 224.64 
L 254.231718 496.44 
L 256.754378 496.44 
L 256.754378 224.64 
L 254.231718 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 256.754378 224.64 
L 256.754378 496.44 
L 257.041829 496.44 
L 257.041829 224.64 
L 256.754378 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.041829 224.64 
L 257.041829 496.44 
L 257.272008 496.44 
L 257.272008 224.64 
L 257.041829 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.272008 224.64 
L 257.272008 496.44 
L 257.437703 496.44 
L 257.437703 224.64 
L 257.272008 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.437703 224.64 
L 257.437703 496.44 
L 257.572121 496.44 
L 257.572121 224.64 
L 257.437703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.572121 224.64 
L 257.572121 496.44 
L 257.682976 496.44 
L 257.682976 224.64 
L 257.572121 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.685156 224.64 
L 257.685156 496.44 
L 257.714505 496.44 
L 257.714505 224.64 
L 257.685156 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.716098 224.64 
L 257.716098 496.44 
L 257.863345 496.44 
L 257.863345 224.64 
L 257.716098 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.863345 224.64 
L 257.863345 496.44 
L 257.907117 496.44 
L 257.907117 224.64 
L 257.863345 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 257.907117 224.64 
L 257.907117 496.44 
L 258.041786 496.44 
L 258.041786 224.64 
L 257.907117 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.041786 224.64 
L 258.041786 496.44 
L 258.156415 496.44 
L 258.156415 224.64 
L 258.041786 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.156415 224.64 
L 258.156415 496.44 
L 258.257626 496.44 
L 258.257626 224.64 
L 258.156415 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.258549 224.64 
L 258.258549 496.44 
L 258.414936 496.44 
L 258.414936 224.64 
L 258.258549 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_97">
    <path clip-path="url(#p9901fb19d8)" d="M 258.417033 224.64 
L 258.417033 496.44 
L 258.540466 496.44 
L 258.540466 224.64 
L 258.417033 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.541304 224.64 
L 258.541304 496.44 
L 258.594468 496.44 
L 258.594468 224.64 
L 258.541304 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.594887 224.64 
L 258.594887 496.44 
L 258.63346 496.44 
L 258.63346 224.64 
L 258.594887 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.635388 224.64 
L 258.635388 496.44 
L 258.740038 496.44 
L 258.740038 224.64 
L 258.635388 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 258.740038 224.64 
L 258.740038 496.44 
L 259.074615 496.44 
L 259.074615 224.64 
L 258.740038 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 259.074615 224.64 
L 259.074615 496.44 
L 260.149957 496.44 
L 260.149957 224.64 
L 259.074615 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.150376 224.64 
L 260.150376 496.44 
L 260.258799 496.44 
L 260.258799 224.64 
L 260.150376 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.258799 224.64 
L 260.258799 496.44 
L 260.401518 496.44 
L 260.401518 224.64 
L 260.258799 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.401518 224.64 
L 260.401518 496.44 
L 260.66113 496.44 
L 260.66113 224.64 
L 260.401518 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 260.66113 224.64 
L 260.66113 496.44 
L 261.204252 496.44 
L 261.204252 224.64 
L 260.66113 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.204252 224.64 
L 261.204252 496.44 
L 261.299593 496.44 
L 261.299593 224.64 
L 261.204252 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.299593 224.64 
L 261.299593 496.44 
L 261.36349 496.44 
L 261.36349 224.64 
L 261.299593 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 261.365838 224.64 
L 261.365838 496.44 
L 262.502142 496.44 
L 262.502142 224.64 
L 261.365838 224.64 
z
" style="fill:#f8efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 262.502561 224.64 
L 262.502561 496.44 
L 263.644986 496.44 
L 263.644986 224.64 
L 262.502561 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.644986 224.64 
L 263.644986 496.44 
L 263.815545 496.44 
L 263.815545 224.64 
L 263.644986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 263.815545 224.64 
L 263.815545 496.44 
L 264.464741 496.44 
L 264.464741 224.64 
L 263.815545 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.464741 224.64 
L 264.464741 496.44 
L 264.633288 496.44 
L 264.633288 224.64 
L 264.464741 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.633288 224.64 
L 264.633288 496.44 
L 264.894241 496.44 
L 264.894241 224.64 
L 264.633288 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 264.894241 224.64 
L 264.894241 496.44 
L 266.024172 496.44 
L 266.024172 224.64 
L 264.894241 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.024927 224.64 
L 266.024927 496.44 
L 266.118256 496.44 
L 266.118256 224.64 
L 266.024927 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.118256 224.64 
L 266.118256 496.44 
L 266.182236 496.44 
L 266.182236 224.64 
L 266.118256 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.182236 224.64 
L 266.182236 496.44 
L 266.449101 496.44 
L 266.449101 224.64 
L 266.182236 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.449101 224.64 
L 266.449101 496.44 
L 266.708923 496.44 
L 266.708923 224.64 
L 266.449101 224.64 
z
" style="fill:#f7f7fb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.708923 224.64 
L 266.708923 496.44 
L 266.733492 496.44 
L 266.733492 224.64 
L 266.708923 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 266.733492 224.64 
L 266.733492 496.44 
L 267.170286 496.44 
L 267.170286 224.64 
L 266.733492 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.170706 224.64 
L 267.170706 496.44 
L 267.386462 496.44 
L 267.386462 224.64 
L 267.170706 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.386462 224.64 
L 267.386462 496.44 
L 267.544191 496.44 
L 267.544191 224.64 
L 267.386462 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.544191 224.64 
L 267.544191 496.44 
L 267.721626 496.44 
L 267.721626 224.64 
L 267.544191 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.721626 224.64 
L 267.721626 496.44 
L 267.866106 496.44 
L 267.866106 224.64 
L 267.721626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 267.866106 224.64 
L 267.866106 496.44 
L 268.088486 496.44 
L 268.088486 224.64 
L 267.866106 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.088906 224.64 
L 268.088906 496.44 
L 268.123873 496.44 
L 268.123873 224.64 
L 268.088906 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.124292 224.64 
L 268.124292 496.44 
L 268.520585 496.44 
L 268.520585 224.64 
L 268.124292 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 268.520585 224.64 
L 268.520585 496.44 
L 269.108317 496.44 
L 269.108317 224.64 
L 268.520585 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.108736 224.64 
L 269.108736 496.44 
L 269.509474 496.44 
L 269.509474 224.64 
L 269.108736 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 269.509474 224.64 
L 269.509474 496.44 
L 269.959182 496.44 
L 269.959182 224.64 
L 269.509474 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.22785 224.64 
L 270.22785 496.44 
L 270.243111 496.44 
L 270.243111 224.64 
L 270.22785 224.64 
z
" style="fill:#9191df;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.256696 224.64 
L 270.256696 496.44 
L 270.28202 496.44 
L 270.28202 224.64 
L 270.256696 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.28202 224.64 
L 270.28202 496.44 
L 270.324617 496.44 
L 270.324617 224.64 
L 270.28202 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.324617 224.64 
L 270.324617 496.44 
L 270.422056 496.44 
L 270.422056 224.64 
L 270.324617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.423649 224.64 
L 270.423649 496.44 
L 270.950419 496.44 
L 270.950419 224.64 
L 270.423649 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 270.950419 224.64 
L 270.950419 496.44 
L 271.491025 496.44 
L 271.491025 224.64 
L 270.950419 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.491025 224.64 
L 271.491025 496.44 
L 271.653198 496.44 
L 271.653198 224.64 
L 271.491025 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.653198 224.64 
L 271.653198 496.44 
L 271.960439 496.44 
L 271.960439 224.64 
L 271.653198 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 271.960439 224.64 
L 271.960439 496.44 
L 272.873859 496.44 
L 272.873859 224.64 
L 271.960439 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.874362 224.64 
L 272.874362 496.44 
L 272.938846 496.44 
L 272.938846 224.64 
L 272.874362 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 272.938846 224.64 
L 272.938846 496.44 
L 273.19351 496.44 
L 273.19351 224.64 
L 272.938846 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.19351 224.64 
L 273.19351 496.44 
L 273.361805 496.44 
L 273.361805 224.64 
L 273.19351 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.361805 224.64 
L 273.361805 496.44 
L 273.967649 496.44 
L 273.967649 224.64 
L 273.361805 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 273.967649 224.64 
L 273.967649 496.44 
L 274.235981 496.44 
L 274.235981 224.64 
L 273.967649 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 274.235981 224.64 
L 274.235981 496.44 
L 276.898174 496.44 
L 276.898174 224.64 
L 274.235981 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 276.898174 224.64 
L 276.898174 496.44 
L 277.170531 496.44 
L 277.170531 224.64 
L 276.898174 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.170531 224.64 
L 277.170531 496.44 
L 277.643215 496.44 
L 277.643215 224.64 
L 277.170531 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.643215 224.64 
L 277.643215 496.44 
L 277.77017 496.44 
L 277.77017 224.64 
L 277.643215 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 277.77017 224.64 
L 277.77017 496.44 
L 278.84199 496.44 
L 278.84199 224.64 
L 277.77017 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.84199 224.64 
L 278.84199 496.44 
L 278.924335 496.44 
L 278.924335 224.64 
L 278.84199 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 278.924335 224.64 
L 278.924335 496.44 
L 279.370018 496.44 
L 279.370018 224.64 
L 278.924335 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.370437 224.64 
L 279.370437 496.44 
L 279.496721 496.44 
L 279.496721 224.64 
L 279.370437 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.496721 224.64 
L 279.496721 496.44 
L 279.881778 496.44 
L 279.881778 224.64 
L 279.496721 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 279.881778 224.64 
L 279.881778 496.44 
L 280.354295 496.44 
L 280.354295 224.64 
L 279.881778 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.354295 224.64 
L 280.354295 496.44 
L 280.573824 496.44 
L 280.573824 224.64 
L 280.354295 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 280.573824 224.64 
L 280.573824 496.44 
L 281.046844 496.44 
L 281.046844 224.64 
L 280.573824 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.046844 224.64 
L 281.046844 496.44 
L 281.377983 496.44 
L 281.377983 224.64 
L 281.046844 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 281.377983 224.64 
L 281.377983 496.44 
L 282.184154 496.44 
L 282.184154 224.64 
L 281.377983 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.184573 224.64 
L 282.184573 496.44 
L 282.222643 496.44 
L 282.222643 224.64 
L 282.184573 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.222643 224.64 
L 282.222643 496.44 
L 282.381462 496.44 
L 282.381462 224.64 
L 282.222643 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.381462 224.64 
L 282.381462 496.44 
L 282.933304 496.44 
L 282.933304 224.64 
L 282.381462 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 282.933304 224.64 
L 282.933304 496.44 
L 283.092459 496.44 
L 283.092459 224.64 
L 282.933304 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.092459 224.64 
L 283.092459 496.44 
L 283.177235 496.44 
L 283.177235 224.64 
L 283.092459 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.177235 224.64 
L 283.177235 496.44 
L 283.815531 496.44 
L 283.815531 224.64 
L 283.177235 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 283.816118 224.64 
L 283.816118 496.44 
L 284.610633 496.44 
L 284.610633 224.64 
L 283.816118 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.610633 224.64 
L 284.610633 496.44 
L 284.678052 496.44 
L 284.678052 224.64 
L 284.610633 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 284.678052 224.64 
L 284.678052 496.44 
L 285.765972 496.44 
L 285.765972 224.64 
L 284.678052 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.765972 224.64 
L 285.765972 496.44 
L 285.897119 496.44 
L 285.897119 224.64 
L 285.765972 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 285.897119 224.64 
L 285.897119 496.44 
L 286.446614 496.44 
L 286.446614 224.64 
L 285.897119 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.446614 224.64 
L 286.446614 496.44 
L 286.682411 496.44 
L 286.682411 224.64 
L 286.446614 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.682411 224.64 
L 286.682411 496.44 
L 286.756873 496.44 
L 286.756873 224.64 
L 286.682411 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.756873 224.64 
L 286.756873 496.44 
L 286.952923 496.44 
L 286.952923 224.64 
L 286.756873 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 286.952923 224.64 
L 286.952923 496.44 
L 287.073505 496.44 
L 287.073505 224.64 
L 286.952923 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.073505 224.64 
L 287.073505 496.44 
L 287.225951 496.44 
L 287.225951 224.64 
L 287.073505 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.225951 224.64 
L 287.225951 496.44 
L 287.49856 496.44 
L 287.49856 224.64 
L 287.225951 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.49856 224.64 
L 287.49856 496.44 
L 287.588368 496.44 
L 287.588368 224.64 
L 287.49856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.588368 224.64 
L 287.588368 496.44 
L 287.686645 496.44 
L 287.686645 224.64 
L 287.588368 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.686645 224.64 
L 287.686645 496.44 
L 287.777207 496.44 
L 287.777207 224.64 
L 287.686645 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 287.777207 224.64 
L 287.777207 496.44 
L 288.304731 496.44 
L 288.304731 224.64 
L 287.777207 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.304731 224.64 
L 288.304731 496.44 
L 288.464473 496.44 
L 288.464473 224.64 
L 288.304731 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.464473 224.64 
L 288.464473 496.44 
L 288.738675 496.44 
L 288.738675 224.64 
L 288.464473 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.738675 224.64 
L 288.738675 496.44 
L 288.754062 496.44 
L 288.754062 224.64 
L 288.738675 224.64 
z
" style="fill:#f5e4e4;"/>
   </g>
   <g id="BrokenBarHCollection_98">
    <path clip-path="url(#p9901fb19d8)" d="M 288.784669 224.64 
L 288.784669 496.44 
L 288.892254 496.44 
L 288.892254 224.64 
L 288.784669 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 288.896363 224.64 
L 288.896363 496.44 
L 289.017532 496.44 
L 289.017532 224.64 
L 288.896363 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.017532 224.64 
L 289.017532 496.44 
L 289.090904 496.44 
L 289.090904 224.64 
L 289.017532 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.090904 224.64 
L 289.090904 496.44 
L 289.272531 496.44 
L 289.272531 224.64 
L 289.090904 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.27295 224.64 
L 289.27295 496.44 
L 289.823535 496.44 
L 289.823535 224.64 
L 289.27295 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 289.823535 224.64 
L 289.823535 496.44 
L 290.08365 496.44 
L 290.08365 224.64 
L 289.823535 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.08365 224.64 
L 290.08365 496.44 
L 290.619979 496.44 
L 290.619979 224.64 
L 290.08365 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.619979 224.64 
L 290.619979 496.44 
L 290.84303 496.44 
L 290.84303 224.64 
L 290.619979 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.84303 224.64 
L 290.84303 496.44 
L 290.935857 496.44 
L 290.935857 224.64 
L 290.84303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 290.935857 224.64 
L 290.935857 496.44 
L 291.596625 496.44 
L 291.596625 224.64 
L 290.935857 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.596625 224.64 
L 291.596625 496.44 
L 291.717123 496.44 
L 291.717123 224.64 
L 291.596625 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 291.717123 224.64 
L 291.717123 496.44 
L 292.188885 496.44 
L 292.188885 224.64 
L 291.717123 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.188885 224.64 
L 292.188885 496.44 
L 292.326992 496.44 
L 292.326992 224.64 
L 292.188885 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.326992 224.64 
L 292.326992 496.44 
L 292.44095 496.44 
L 292.44095 224.64 
L 292.326992 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.44095 224.64 
L 292.44095 496.44 
L 292.887639 496.44 
L 292.887639 224.64 
L 292.44095 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.887639 224.64 
L 292.887639 496.44 
L 292.915395 496.44 
L 292.915395 224.64 
L 292.887639 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 292.916149 224.64 
L 292.916149 496.44 
L 293.116392 496.44 
L 293.116392 224.64 
L 292.916149 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.116392 224.64 
L 293.116392 496.44 
L 293.250056 496.44 
L 293.250056 224.64 
L 293.116392 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.250056 224.64 
L 293.250056 496.44 
L 293.735821 496.44 
L 293.735821 224.64 
L 293.250056 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 293.735821 224.64 
L 293.735821 496.44 
L 294.019331 496.44 
L 294.019331 224.64 
L 293.735821 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.01975 224.64 
L 294.01975 496.44 
L 294.199868 496.44 
L 294.199868 224.64 
L 294.01975 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.200288 224.64 
L 294.200288 496.44 
L 294.292778 496.44 
L 294.292778 224.64 
L 294.200288 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.293198 224.64 
L 294.293198 496.44 
L 294.338898 496.44 
L 294.338898 224.64 
L 294.293198 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.338898 224.64 
L 294.338898 496.44 
L 294.394242 496.44 
L 294.394242 224.64 
L 294.338898 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.394242 224.64 
L 294.394242 496.44 
L 294.472393 496.44 
L 294.472393 224.64 
L 294.394242 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.472393 224.64 
L 294.472393 496.44 
L 294.593981 496.44 
L 294.593981 224.64 
L 294.472393 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 294.593981 224.64 
L 294.593981 496.44 
L 295.168967 496.44 
L 295.168967 224.64 
L 294.593981 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.168967 224.64 
L 295.168967 496.44 
L 295.599725 496.44 
L 295.599725 224.64 
L 295.168967 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.599725 224.64 
L 295.599725 496.44 
L 295.75955 496.44 
L 295.75955 224.64 
L 295.599725 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 295.75955 224.64 
L 295.75955 496.44 
L 296.08222 496.44 
L 296.08222 224.64 
L 295.75955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.08222 224.64 
L 296.08222 496.44 
L 296.14444 496.44 
L 296.14444 224.64 
L 296.08222 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.14444 224.64 
L 296.14444 496.44 
L 296.617124 496.44 
L 296.617124 224.64 
L 296.14444 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.617124 224.64 
L 296.617124 496.44 
L 296.754309 496.44 
L 296.754309 224.64 
L 296.617124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 296.754309 224.64 
L 296.754309 496.44 
L 298.215882 496.44 
L 298.215882 224.64 
L 296.754309 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.215882 224.64 
L 298.215882 496.44 
L 298.366986 496.44 
L 298.366986 224.64 
L 298.215882 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.366986 224.64 
L 298.366986 496.44 
L 298.611253 496.44 
L 298.611253 224.64 
L 298.366986 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.611253 224.64 
L 298.611253 496.44 
L 298.871912 496.44 
L 298.871912 224.64 
L 298.611253 224.64 
z
" style="fill:#bebeeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 298.871912 224.64 
L 298.871912 496.44 
L 299.194624 496.44 
L 299.194624 224.64 
L 298.871912 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 299.194624 224.64 
L 299.194624 496.44 
L 300.663995 496.44 
L 300.663995 224.64 
L 299.194624 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.663995 224.64 
L 300.663995 496.44 
L 300.746424 496.44 
L 300.746424 224.64 
L 300.663995 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 300.746424 224.64 
L 300.746424 496.44 
L 301.014337 496.44 
L 301.014337 224.64 
L 300.746424 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.014337 224.64 
L 301.014337 496.44 
L 301.236717 496.44 
L 301.236717 224.64 
L 301.014337 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.236717 224.64 
L 301.236717 496.44 
L 301.463877 496.44 
L 301.463877 224.64 
L 301.236717 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.463877 224.64 
L 301.463877 496.44 
L 301.68391 496.44 
L 301.68391 224.64 
L 301.463877 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 301.684748 224.64 
L 301.684748 496.44 
L 302.443374 496.44 
L 302.443374 224.64 
L 301.684748 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.443961 224.64 
L 302.443961 496.44 
L 302.645798 496.44 
L 302.645798 224.64 
L 302.443961 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.645798 224.64 
L 302.645798 496.44 
L 302.934003 496.44 
L 302.934003 224.64 
L 302.645798 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 302.934003 224.64 
L 302.934003 496.44 
L 303.062719 496.44 
L 303.062719 224.64 
L 302.934003 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.063558 224.64 
L 303.063558 496.44 
L 303.281494 496.44 
L 303.281494 224.64 
L 303.063558 224.64 
z
" style="fill:#5f5fd4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.281997 224.64 
L 303.281997 496.44 
L 303.295917 496.44 
L 303.295917 224.64 
L 303.281997 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.296671 224.64 
L 303.296671 496.44 
L 303.517794 496.44 
L 303.517794 224.64 
L 303.296671 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 303.517794 224.64 
L 303.517794 496.44 
L 304.016221 496.44 
L 304.016221 224.64 
L 303.517794 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.016221 224.64 
L 304.016221 496.44 
L 304.506934 496.44 
L 304.506934 224.64 
L 304.016221 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.506934 224.64 
L 304.506934 496.44 
L 304.957733 496.44 
L 304.957733 224.64 
L 304.506934 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 304.957733 224.64 
L 304.957733 496.44 
L 305.489366 496.44 
L 305.489366 224.64 
L 304.957733 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.489366 224.64 
L 305.489366 496.44 
L 305.784867 496.44 
L 305.784867 224.64 
L 305.489366 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 305.784867 224.64 
L 305.784867 496.44 
L 306.179232 496.44 
L 306.179232 224.64 
L 305.784867 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.179232 224.64 
L 306.179232 496.44 
L 306.353229 496.44 
L 306.353229 224.64 
L 306.179232 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.353732 224.64 
L 306.353732 496.44 
L 306.407063 496.44 
L 306.407063 224.64 
L 306.353732 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.40765 224.64 
L 306.40765 496.44 
L 306.540894 496.44 
L 306.540894 224.64 
L 306.40765 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.540894 224.64 
L 306.540894 496.44 
L 306.720928 496.44 
L 306.720928 224.64 
L 306.540894 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.720928 224.64 
L 306.720928 496.44 
L 306.828596 496.44 
L 306.828596 224.64 
L 306.720928 224.64 
z
" style="fill:#5050d0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.828596 224.64 
L 306.828596 496.44 
L 306.993453 496.44 
L 306.993453 224.64 
L 306.828596 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 306.993453 224.64 
L 306.993453 496.44 
L 307.276292 496.44 
L 307.276292 224.64 
L 306.993453 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.276292 224.64 
L 307.276292 496.44 
L 307.574979 496.44 
L 307.574979 224.64 
L 307.276292 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.575902 224.64 
L 307.575902 496.44 
L 307.70923 496.44 
L 307.70923 224.64 
L 307.575902 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 307.710236 224.64 
L 307.710236 496.44 
L 308.011607 496.44 
L 308.011607 224.64 
L 307.710236 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.011607 224.64 
L 308.011607 496.44 
L 308.191305 496.44 
L 308.191305 224.64 
L 308.011607 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.191305 224.64 
L 308.191305 496.44 
L 308.356581 496.44 
L 308.356581 224.64 
L 308.191305 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.356581 224.64 
L 308.356581 496.44 
L 308.486303 496.44 
L 308.486303 224.64 
L 308.356581 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 308.486303 224.64 
L 308.486303 496.44 
L 309.140783 496.44 
L 309.140783 224.64 
L 308.486303 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.140783 224.64 
L 309.140783 496.44 
L 309.224133 496.44 
L 309.224133 224.64 
L 309.140783 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.224133 224.64 
L 309.224133 496.44 
L 309.589988 496.44 
L 309.589988 224.64 
L 309.224133 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.589988 224.64 
L 309.589988 496.44 
L 309.849683 496.44 
L 309.849683 224.64 
L 309.589988 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 309.849683 224.64 
L 309.849683 496.44 
L 310.617114 496.44 
L 310.617114 224.64 
L 309.849683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.617114 224.64 
L 310.617114 496.44 
L 310.940035 496.44 
L 310.940035 224.64 
L 310.617114 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 310.940035 224.64 
L 310.940035 496.44 
L 311.407185 496.44 
L 311.407185 224.64 
L 310.940035 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.407185 224.64 
L 311.407185 496.44 
L 311.627134 496.44 
L 311.627134 224.64 
L 311.407185 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.627134 224.64 
L 311.627134 496.44 
L 311.999697 496.44 
L 311.999697 224.64 
L 311.627134 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 311.999697 224.64 
L 311.999697 496.44 
L 312.622982 496.44 
L 312.622982 224.64 
L 311.999697 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 312.623402 224.64 
L 312.623402 496.44 
L 313.018521 496.44 
L 313.018521 224.64 
L 312.623402 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.018521 224.64 
L 313.018521 496.44 
L 313.168619 496.44 
L 313.168619 224.64 
L 313.018521 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.168619 224.64 
L 313.168619 496.44 
L 313.527095 496.44 
L 313.527095 224.64 
L 313.168619 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.527095 224.64 
L 313.527095 496.44 
L 313.671659 496.44 
L 313.671659 224.64 
L 313.527095 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.671659 224.64 
L 313.671659 496.44 
L 313.712412 496.44 
L 313.712412 224.64 
L 313.671659 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.712412 224.64 
L 313.712412 496.44 
L 313.804483 496.44 
L 313.804483 224.64 
L 313.712412 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.804483 224.64 
L 313.804483 496.44 
L 313.882971 496.44 
L 313.882971 224.64 
L 313.804483 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 313.882971 224.64 
L 313.882971 496.44 
L 314.02418 496.44 
L 314.02418 224.64 
L 313.882971 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.02418 224.64 
L 314.02418 496.44 
L 314.175453 496.44 
L 314.175453 224.64 
L 314.02418 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.175453 224.64 
L 314.175453 496.44 
L 314.401942 496.44 
L 314.401942 224.64 
L 314.175453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.401942 224.64 
L 314.401942 496.44 
L 314.742137 496.44 
L 314.742137 224.64 
L 314.401942 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.742137 224.64 
L 314.742137 496.44 
L 314.807208 496.44 
L 314.807208 224.64 
L 314.742137 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 314.807627 224.64 
L 314.807627 496.44 
L 315.448942 496.44 
L 315.448942 224.64 
L 314.807627 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.448942 224.64 
L 315.448942 496.44 
L 315.739914 496.44 
L 315.739914 224.64 
L 315.448942 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 315.739914 224.64 
L 315.739914 496.44 
L 316.014368 496.44 
L 316.014368 224.64 
L 315.739914 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.014368 224.64 
L 316.014368 496.44 
L 316.717315 496.44 
L 316.717315 224.64 
L 316.014368 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.717315 224.64 
L 316.717315 496.44 
L 316.878063 496.44 
L 316.878063 224.64 
L 316.717315 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.878063 224.64 
L 316.878063 496.44 
L 316.989756 496.44 
L 316.989756 224.64 
L 316.878063 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 316.989756 224.64 
L 316.989756 496.44 
L 317.162495 496.44 
L 317.162495 224.64 
L 316.989756 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.162495 224.64 
L 317.162495 496.44 
L 317.419675 496.44 
L 317.419675 224.64 
L 317.162495 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.420094 224.64 
L 317.420094 496.44 
L 317.43502 496.44 
L 317.43502 224.64 
L 317.420094 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_99">
    <path clip-path="url(#p9901fb19d8)" d="M 317.440807 224.64 
L 317.440807 496.44 
L 317.460261 496.44 
L 317.460261 224.64 
L 317.440807 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.461938 224.64 
L 317.461938 496.44 
L 317.603567 496.44 
L 317.603567 224.64 
L 317.461938 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.603567 224.64 
L 317.603567 496.44 
L 317.633838 496.44 
L 317.633838 224.64 
L 317.603567 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.634257 224.64 
L 317.634257 496.44 
L 317.749808 496.44 
L 317.749808 224.64 
L 317.634257 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.749808 224.64 
L 317.749808 496.44 
L 317.922212 496.44 
L 317.922212 224.64 
L 317.749808 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 317.922212 224.64 
L 317.922212 496.44 
L 318.210417 496.44 
L 318.210417 224.64 
L 317.922212 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.213017 224.64 
L 318.213017 496.44 
L 318.578536 496.44 
L 318.578536 224.64 
L 318.213017 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 318.586754 224.64 
L 318.586754 496.44 
L 319.078724 496.44 
L 319.078724 224.64 
L 318.586754 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.079479 224.64 
L 319.079479 496.44 
L 319.193185 496.44 
L 319.193185 224.64 
L 319.079479 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.193185 224.64 
L 319.193185 496.44 
L 319.385462 496.44 
L 319.385462 224.64 
L 319.193185 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 319.385462 224.64 
L 319.385462 496.44 
L 320.045979 496.44 
L 320.045979 224.64 
L 319.385462 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.046398 224.64 
L 320.046398 496.44 
L 320.419799 496.44 
L 320.419799 224.64 
L 320.046398 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.419799 224.64 
L 320.419799 496.44 
L 320.655848 496.44 
L 320.655848 224.64 
L 320.419799 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 320.655848 224.64 
L 320.655848 496.44 
L 321.857138 496.44 
L 321.857138 224.64 
L 320.655848 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 321.857138 224.64 
L 321.857138 496.44 
L 322.005643 496.44 
L 322.005643 224.64 
L 321.857138 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.005643 224.64 
L 322.005643 496.44 
L 322.279762 496.44 
L 322.279762 224.64 
L 322.005643 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.279762 224.64 
L 322.279762 496.44 
L 322.476399 496.44 
L 322.476399 224.64 
L 322.279762 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.476399 224.64 
L 322.476399 496.44 
L 322.561511 496.44 
L 322.561511 224.64 
L 322.476399 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 322.561511 224.64 
L 322.561511 496.44 
L 323.346131 496.44 
L 323.346131 224.64 
L 322.561511 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.346131 224.64 
L 323.346131 496.44 
L 323.47644 496.44 
L 323.47644 224.64 
L 323.346131 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.47644 224.64 
L 323.47644 496.44 
L 323.859485 496.44 
L 323.859485 224.64 
L 323.47644 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.859485 224.64 
L 323.859485 496.44 
L 323.869547 496.44 
L 323.869547 224.64 
L 323.859485 224.64 
z
" style="fill:#c31313;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 323.874495 224.64 
L 323.874495 496.44 
L 324.060482 496.44 
L 324.060482 224.64 
L 323.874495 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.060482 224.64 
L 324.060482 496.44 
L 324.542139 496.44 
L 324.542139 224.64 
L 324.060482 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.542139 224.64 
L 324.542139 496.44 
L 324.8446 496.44 
L 324.8446 224.64 
L 324.542139 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.8446 224.64 
L 324.8446 496.44 
L 324.911683 496.44 
L 324.911683 224.64 
L 324.8446 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 324.911683 224.64 
L 324.911683 496.44 
L 325.10832 496.44 
L 325.10832 224.64 
L 324.911683 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.10832 224.64 
L 325.10832 496.44 
L 325.134147 496.44 
L 325.134147 224.64 
L 325.10832 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.134147 224.64 
L 325.134147 496.44 
L 325.329359 496.44 
L 325.329359 224.64 
L 325.134147 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.329359 224.64 
L 325.329359 496.44 
L 325.479793 496.44 
L 325.479793 224.64 
L 325.329359 224.64 
z
" style="fill:#e09595;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.479793 224.64 
L 325.479793 496.44 
L 325.968997 496.44 
L 325.968997 224.64 
L 325.479793 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 325.968997 224.64 
L 325.968997 496.44 
L 326.087817 496.44 
L 326.087817 224.64 
L 325.968997 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.088488 224.64 
L 326.088488 496.44 
L 326.244456 496.44 
L 326.244456 224.64 
L 326.088488 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.244456 224.64 
L 326.244456 496.44 
L 326.568803 496.44 
L 326.568803 224.64 
L 326.244456 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.569223 224.64 
L 326.569223 496.44 
L 326.766028 496.44 
L 326.766028 224.64 
L 326.569223 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 326.766028 224.64 
L 326.766028 496.44 
L 327.005514 496.44 
L 327.005514 224.64 
L 326.766028 224.64 
z
" style="fill:#df8f8f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.009204 224.64 
L 327.009204 496.44 
L 327.078802 496.44 
L 327.078802 224.64 
L 327.009204 224.64 
z
" style="fill:#df8e8e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.079222 224.64 
L 327.079222 496.44 
L 327.106894 496.44 
L 327.106894 224.64 
L 327.079222 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.11117 224.64 
L 327.11117 496.44 
L 327.146305 496.44 
L 327.146305 224.64 
L 327.11117 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.146724 224.64 
L 327.146724 496.44 
L 327.422729 496.44 
L 327.422729 224.64 
L 327.146724 224.64 
z
" style="fill:#e6adad;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.422729 224.64 
L 327.422729 496.44 
L 327.682131 496.44 
L 327.682131 224.64 
L 327.422729 224.64 
z
" style="fill:#e3a0a0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.706029 224.64 
L 327.706029 496.44 
L 327.730012 496.44 
L 327.730012 224.64 
L 327.706029 224.64 
z
" style="fill:#e4a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.741835 224.64 
L 327.741835 496.44 
L 327.765314 496.44 
L 327.765314 224.64 
L 327.741835 224.64 
z
" style="fill:#e39f9f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.767662 224.64 
L 327.767662 496.44 
L 327.818897 496.44 
L 327.818897 224.64 
L 327.767662 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.818897 224.64 
L 327.818897 496.44 
L 327.837428 496.44 
L 327.837428 224.64 
L 327.818897 224.64 
z
" style="fill:#eecccc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.837428 224.64 
L 327.837428 496.44 
L 327.959855 496.44 
L 327.959855 224.64 
L 327.837428 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 327.966396 224.64 
L 327.966396 496.44 
L 327.982999 496.44 
L 327.982999 224.64 
L 327.966396 224.64 
z
" style="fill:#e7b0b0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.003962 224.64 
L 328.003962 496.44 
L 328.266257 496.44 
L 328.266257 224.64 
L 328.003962 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.266257 224.64 
L 328.266257 496.44 
L 328.276907 496.44 
L 328.276907 224.64 
L 328.266257 224.64 
z
" style="fill:#d15353;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.276907 224.64 
L 328.276907 496.44 
L 328.288814 496.44 
L 328.288814 224.64 
L 328.276907 224.64 
z
" style="fill:#de8b8b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.290155 224.64 
L 328.290155 496.44 
L 328.352123 496.44 
L 328.352123 224.64 
L 328.290155 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.352123 224.64 
L 328.352123 496.44 
L 328.36185 496.44 
L 328.36185 224.64 
L 328.352123 224.64 
z
" style="fill:#eabdbd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.36185 224.64 
L 328.36185 496.44 
L 328.642426 496.44 
L 328.642426 224.64 
L 328.36185 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.642426 224.64 
L 328.642426 496.44 
L 328.817764 496.44 
L 328.817764 224.64 
L 328.642426 224.64 
z
" style="fill:#e39e9e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.818183 224.64 
L 328.818183 496.44 
L 328.946564 496.44 
L 328.946564 224.64 
L 328.818183 224.64 
z
" style="fill:#e4a5a5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 328.946564 224.64 
L 328.946564 496.44 
L 329.021613 496.44 
L 329.021613 224.64 
L 328.946564 224.64 
z
" style="fill:#e9b8b8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.021613 224.64 
L 329.021613 496.44 
L 329.085174 496.44 
L 329.085174 224.64 
L 329.021613 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.085593 224.64 
L 329.085593 496.44 
L 329.217915 496.44 
L 329.217915 224.64 
L 329.085593 224.64 
z
" style="fill:#e3a2a2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.217915 224.64 
L 329.217915 496.44 
L 329.511403 496.44 
L 329.511403 224.64 
L 329.217915 224.64 
z
" style="fill:#e7afaf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.511403 224.64 
L 329.511403 496.44 
L 329.589974 496.44 
L 329.589974 224.64 
L 329.511403 224.64 
z
" style="fill:#df9292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.589974 224.64 
L 329.589974 496.44 
L 329.603139 496.44 
L 329.603139 224.64 
L 329.589974 224.64 
z
" style="fill:#eabbbb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.614879 224.64 
L 329.614879 496.44 
L 329.888326 496.44 
L 329.888326 224.64 
L 329.614879 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.898892 224.64 
L 329.898892 496.44 
L 329.914908 496.44 
L 329.914908 224.64 
L 329.898892 224.64 
z
" style="fill:#d15454;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.922036 224.64 
L 329.922036 496.44 
L 329.943167 496.44 
L 329.943167 224.64 
L 329.922036 224.64 
z
" style="fill:#d35b5b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.962956 224.64 
L 329.962956 496.44 
L 329.974193 496.44 
L 329.974193 224.64 
L 329.962956 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 329.977211 224.64 
L 329.977211 496.44 
L 329.988364 496.44 
L 329.988364 224.64 
L 329.977211 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.018216 224.64 
L 330.018216 496.44 
L 330.205126 496.44 
L 330.205126 224.64 
L 330.018216 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.209067 224.64 
L 330.209067 496.44 
L 330.29334 496.44 
L 330.29334 224.64 
L 330.209067 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.296108 224.64 
L 330.296108 496.44 
L 330.360591 496.44 
L 330.360591 224.64 
L 330.296108 224.64 
z
" style="fill:#d56666;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.360591 224.64 
L 330.360591 496.44 
L 330.72653 496.44 
L 330.72653 224.64 
L 330.360591 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 330.726949 224.64 
L 330.726949 496.44 
L 332.448133 496.44 
L 332.448133 224.64 
L 330.726949 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.450146 224.64 
L 332.450146 496.44 
L 332.523602 496.44 
L 332.523602 224.64 
L 332.450146 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.523602 224.64 
L 332.523602 496.44 
L 332.837048 496.44 
L 332.837048 224.64 
L 332.523602 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 332.837048 224.64 
L 332.837048 496.44 
L 333.086681 496.44 
L 333.086681 224.64 
L 332.837048 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.087519 224.64 
L 333.087519 496.44 
L 333.863838 496.44 
L 333.863838 224.64 
L 333.087519 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.863838 224.64 
L 333.863838 496.44 
L 333.957503 496.44 
L 333.957503 224.64 
L 333.863838 224.64 
z
" style="fill:#e09494;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 333.957503 224.64 
L 333.957503 496.44 
L 334.34147 496.44 
L 334.34147 224.64 
L 333.957503 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.34147 224.64 
L 334.34147 496.44 
L 334.425491 496.44 
L 334.425491 224.64 
L 334.34147 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.428594 224.64 
L 334.428594 496.44 
L 334.561335 496.44 
L 334.561335 224.64 
L 334.428594 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.561335 224.64 
L 334.561335 496.44 
L 334.578776 496.44 
L 334.578776 224.64 
L 334.561335 224.64 
z
" style="fill:#edc9c9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.579196 224.64 
L 334.579196 496.44 
L 334.590013 496.44 
L 334.590013 224.64 
L 334.579196 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.596469 224.64 
L 334.596469 496.44 
L 334.689715 496.44 
L 334.689715 224.64 
L 334.596469 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.689715 224.64 
L 334.689715 496.44 
L 334.985467 496.44 
L 334.985467 224.64 
L 334.689715 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 334.985467 224.64 
L 334.985467 496.44 
L 335.190826 496.44 
L 335.190826 224.64 
L 334.985467 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.190826 224.64 
L 335.190826 496.44 
L 335.249607 496.44 
L 335.249607 224.64 
L 335.190826 224.64 
z
" style="fill:#d25959;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.249607 224.64 
L 335.249607 496.44 
L 335.788452 496.44 
L 335.788452 224.64 
L 335.249607 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 335.791303 224.64 
L 335.791303 496.44 
L 336.029364 496.44 
L 336.029364 224.64 
L 335.791303 224.64 
z
" style="fill:#d97676;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.029364 224.64 
L 336.029364 496.44 
L 336.118836 496.44 
L 336.118836 224.64 
L 336.029364 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.118836 224.64 
L 336.118836 496.44 
L 336.486619 496.44 
L 336.486619 224.64 
L 336.118836 224.64 
z
" style="fill:#d87070;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 336.486619 224.64 
L 336.486619 496.44 
L 337.246252 496.44 
L 337.246252 224.64 
L 336.486619 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.246252 224.64 
L 337.246252 496.44 
L 337.733191 496.44 
L 337.733191 224.64 
L 337.246252 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 337.733191 224.64 
L 337.733191 496.44 
L 338.038251 496.44 
L 338.038251 224.64 
L 337.733191 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.038671 224.64 
L 338.038671 496.44 
L 338.573826 496.44 
L 338.573826 224.64 
L 338.038671 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.574916 224.64 
L 338.574916 496.44 
L 338.771134 496.44 
L 338.771134 224.64 
L 338.574916 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.771134 224.64 
L 338.771134 496.44 
L 338.899095 496.44 
L 338.899095 224.64 
L 338.771134 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 338.899095 224.64 
L 338.899095 496.44 
L 339.43945 496.44 
L 339.43945 224.64 
L 338.899095 224.64 
z
" style="fill:#db7d7d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.43945 224.64 
L 339.43945 496.44 
L 339.73319 496.44 
L 339.73319 224.64 
L 339.43945 224.64 
z
" style="fill:#df9191;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.73319 224.64 
L 339.73319 496.44 
L 339.872387 496.44 
L 339.872387 224.64 
L 339.73319 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.874064 224.64 
L 339.874064 496.44 
L 339.945675 496.44 
L 339.945675 224.64 
L 339.874064 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 339.945675 224.64 
L 339.945675 496.44 
L 340.099212 496.44 
L 340.099212 224.64 
L 339.945675 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.099799 224.64 
L 340.099799 496.44 
L 340.172919 496.44 
L 340.172919 224.64 
L 340.099799 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.173339 224.64 
L 340.173339 496.44 
L 340.528795 496.44 
L 340.528795 224.64 
L 340.173339 224.64 
z
" style="fill:#d87373;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.528795 224.64 
L 340.528795 496.44 
L 340.78891 496.44 
L 340.78891 224.64 
L 340.528795 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.78891 224.64 
L 340.78891 496.44 
L 340.919638 496.44 
L 340.919638 224.64 
L 340.78891 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 340.919638 224.64 
L 340.919638 496.44 
L 341.266122 496.44 
L 341.266122 224.64 
L 340.919638 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.266122 224.64 
L 341.266122 496.44 
L 341.305366 496.44 
L 341.305366 224.64 
L 341.266122 224.64 
z
" style="fill:#d35a5a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.305366 224.64 
L 341.305366 496.44 
L 341.329264 496.44 
L 341.329264 224.64 
L 341.305366 224.64 
z
" style="fill:#ca3232;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.332367 224.64 
L 341.332367 496.44 
L 341.458818 496.44 
L 341.458818 224.64 
L 341.332367 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.512904 224.64 
L 341.512904 496.44 
L 341.583341 496.44 
L 341.583341 224.64 
L 341.512904 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 341.586612 224.64 
L 341.586612 496.44 
L 342.176356 496.44 
L 342.176356 224.64 
L 341.586612 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.176356 224.64 
L 342.176356 496.44 
L 342.363182 496.44 
L 342.363182 224.64 
L 342.176356 224.64 
z
" style="fill:#df9090;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.363602 224.64 
L 342.363602 496.44 
L 342.417436 496.44 
L 342.417436 224.64 
L 342.363602 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.417436 224.64 
L 342.417436 496.44 
L 342.908819 496.44 
L 342.908819 224.64 
L 342.417436 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 342.908819 224.64 
L 342.908819 496.44 
L 343.327837 496.44 
L 343.327837 224.64 
L 342.908819 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.329095 224.64 
L 343.329095 496.44 
L 343.363978 496.44 
L 343.363978 224.64 
L 343.329095 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.363978 224.64 
L 343.363978 496.44 
L 343.524055 496.44 
L 343.524055 224.64 
L 343.363978 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.524055 224.64 
L 343.524055 496.44 
L 343.662414 496.44 
L 343.662414 224.64 
L 343.524055 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.663588 224.64 
L 343.663588 496.44 
L 343.884543 496.44 
L 343.884543 224.64 
L 343.663588 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 343.884543 224.64 
L 343.884543 496.44 
L 344.122059 496.44 
L 344.122059 224.64 
L 343.884543 224.64 
z
" style="fill:#dd8787;"/>
   </g>
   <g id="BrokenBarHCollection_100">
    <path clip-path="url(#p9901fb19d8)" d="M 344.123778 224.64 
L 344.123778 496.44 
L 344.132625 496.44 
L 344.132625 224.64 
L 344.123778 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.133883 224.64 
L 344.133883 496.44 
L 344.347459 496.44 
L 344.347459 224.64 
L 344.133883 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 344.349052 224.64 
L 344.349052 496.44 
L 345.123191 496.44 
L 345.123191 224.64 
L 344.349052 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.12361 224.64 
L 345.12361 496.44 
L 345.174845 496.44 
L 345.174845 224.64 
L 345.12361 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.174845 224.64 
L 345.174845 496.44 
L 345.315132 496.44 
L 345.315132 224.64 
L 345.174845 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.321337 224.64 
L 345.321337 496.44 
L 345.350267 496.44 
L 345.350267 224.64 
L 345.321337 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.367541 224.64 
L 345.367541 496.44 
L 345.392446 496.44 
L 345.392446 224.64 
L 345.367541 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.392865 224.64 
L 345.392865 496.44 
L 345.405359 496.44 
L 345.405359 224.64 
L 345.392865 224.64 
z
" style="fill:#f4dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.405359 224.64 
L 345.405359 496.44 
L 345.43018 496.44 
L 345.43018 224.64 
L 345.405359 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.440578 224.64 
L 345.440578 496.44 
L 345.460032 496.44 
L 345.460032 224.64 
L 345.440578 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.460032 224.64 
L 345.460032 496.44 
L 345.815656 496.44 
L 345.815656 224.64 
L 345.460032 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 345.815656 224.64 
L 345.815656 496.44 
L 346.118201 496.44 
L 346.118201 224.64 
L 345.815656 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.129773 224.64 
L 346.129773 496.44 
L 346.163063 496.44 
L 346.163063 224.64 
L 346.129773 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.163482 224.64 
L 346.163482 496.44 
L 346.188806 496.44 
L 346.188806 224.64 
L 346.163482 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.189225 224.64 
L 346.189225 496.44 
L 346.257566 496.44 
L 346.257566 224.64 
L 346.189225 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.257566 224.64 
L 346.257566 496.44 
L 346.394667 496.44 
L 346.394667 224.64 
L 346.257566 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 346.394667 224.64 
L 346.394667 496.44 
L 347.189099 496.44 
L 347.189099 224.64 
L 346.394667 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.189099 224.64 
L 347.189099 496.44 
L 347.361167 496.44 
L 347.361167 224.64 
L 347.189099 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.361167 224.64 
L 347.361167 496.44 
L 347.50288 496.44 
L 347.50288 224.64 
L 347.361167 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.50288 224.64 
L 347.50288 496.44 
L 347.705806 496.44 
L 347.705806 224.64 
L 347.50288 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.705806 224.64 
L 347.705806 496.44 
L 347.880977 496.44 
L 347.880977 224.64 
L 347.705806 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 347.880977 224.64 
L 347.880977 496.44 
L 348.056231 496.44 
L 348.056231 224.64 
L 347.880977 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 348.056231 224.64 
L 348.056231 496.44 
L 349.171907 496.44 
L 349.171907 224.64 
L 348.056231 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.171907 224.64 
L 349.171907 496.44 
L 349.688698 496.44 
L 349.688698 224.64 
L 349.171907 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.688698 224.64 
L 349.688698 496.44 
L 349.755782 496.44 
L 349.755782 224.64 
L 349.688698 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 349.755782 224.64 
L 349.755782 496.44 
L 350.513569 496.44 
L 350.513569 224.64 
L 349.755782 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.513569 224.64 
L 350.513569 496.44 
L 350.786346 496.44 
L 350.786346 224.64 
L 350.513569 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 350.786346 224.64 
L 350.786346 496.44 
L 351.024323 496.44 
L 351.024323 224.64 
L 350.786346 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.024323 224.64 
L 351.024323 496.44 
L 351.247123 496.44 
L 351.247123 224.64 
L 351.024323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.247123 224.64 
L 351.247123 496.44 
L 351.460615 496.44 
L 351.460615 224.64 
L 351.247123 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.460615 224.64 
L 351.460615 496.44 
L 351.471264 496.44 
L 351.471264 224.64 
L 351.460615 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.471264 224.64 
L 351.471264 496.44 
L 351.725719 496.44 
L 351.725719 224.64 
L 351.471264 224.64 
z
" style="fill:#cbcbee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.725719 224.64 
L 351.725719 496.44 
L 351.980257 496.44 
L 351.980257 224.64 
L 351.725719 224.64 
z
" style="fill:#c1c1eb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.980257 224.64 
L 351.980257 496.44 
L 351.989397 496.44 
L 351.989397 224.64 
L 351.980257 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 351.989397 224.64 
L 351.989397 496.44 
L 352.204231 496.44 
L 352.204231 224.64 
L 351.989397 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.20465 224.64 
L 352.20465 496.44 
L 352.308293 496.44 
L 352.308293 224.64 
L 352.20465 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.308293 224.64 
L 352.308293 496.44 
L 352.493191 496.44 
L 352.493191 224.64 
L 352.308293 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 352.493191 224.64 
L 352.493191 496.44 
L 353.079665 496.44 
L 353.079665 224.64 
L 352.493191 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.079665 224.64 
L 353.079665 496.44 
L 353.322422 496.44 
L 353.322422 224.64 
L 353.079665 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.322841 224.64 
L 353.322841 496.44 
L 353.457259 496.44 
L 353.457259 224.64 
L 353.322841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.457259 224.64 
L 353.457259 496.44 
L 353.921893 496.44 
L 353.921893 224.64 
L 353.457259 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.922313 224.64 
L 353.922313 496.44 
L 353.999794 496.44 
L 353.999794 224.64 
L 353.922313 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 353.999794 224.64 
L 353.999794 496.44 
L 354.164231 496.44 
L 354.164231 224.64 
L 353.999794 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.164231 224.64 
L 354.164231 496.44 
L 354.447909 496.44 
L 354.447909 224.64 
L 354.164231 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.447909 224.64 
L 354.447909 496.44 
L 354.708275 496.44 
L 354.708275 224.64 
L 354.447909 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 354.708694 224.64 
L 354.708694 496.44 
L 355.045032 496.44 
L 355.045032 224.64 
L 354.708694 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.045032 224.64 
L 355.045032 496.44 
L 355.306908 496.44 
L 355.306908 224.64 
L 355.045032 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.306908 224.64 
L 355.306908 496.44 
L 355.417595 496.44 
L 355.417595 224.64 
L 355.306908 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.417595 224.64 
L 355.417595 496.44 
L 355.553773 496.44 
L 355.553773 224.64 
L 355.417595 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.553773 224.64 
L 355.553773 496.44 
L 355.812463 496.44 
L 355.812463 224.64 
L 355.553773 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.812463 224.64 
L 355.812463 496.44 
L 355.982183 496.44 
L 355.982183 224.64 
L 355.812463 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 355.982183 224.64 
L 355.982183 496.44 
L 356.032998 496.44 
L 356.032998 224.64 
L 355.982183 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.032998 224.64 
L 356.032998 496.44 
L 356.251605 496.44 
L 356.251605 224.64 
L 356.032998 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.251605 224.64 
L 356.251605 496.44 
L 356.437509 496.44 
L 356.437509 224.64 
L 356.251605 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 356.437509 224.64 
L 356.437509 496.44 
L 357.013753 496.44 
L 357.013753 224.64 
L 356.437509 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.013753 224.64 
L 357.013753 496.44 
L 357.394701 496.44 
L 357.394701 224.64 
L 357.013753 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.394701 224.64 
L 357.394701 496.44 
L 357.716868 496.44 
L 357.716868 224.64 
L 357.394701 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.716868 224.64 
L 357.716868 496.44 
L 357.7972 496.44 
L 357.7972 224.64 
L 357.716868 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.7972 224.64 
L 357.7972 496.44 
L 357.974048 496.44 
L 357.974048 224.64 
L 357.7972 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 357.974467 224.64 
L 357.974467 496.44 
L 358.520775 496.44 
L 358.520775 224.64 
L 357.974467 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.520775 224.64 
L 358.520775 496.44 
L 358.667016 496.44 
L 358.667016 224.64 
L 358.520775 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.668609 224.64 
L 358.668609 496.44 
L 358.67842 496.44 
L 358.67842 224.64 
L 358.668609 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.68538 224.64 
L 358.68538 496.44 
L 358.823823 496.44 
L 358.823823 224.64 
L 358.68538 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 358.823823 224.64 
L 358.823823 496.44 
L 359.95476 496.44 
L 359.95476 224.64 
L 358.823823 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 359.95476 224.64 
L 359.95476 496.44 
L 360.447234 496.44 
L 360.447234 224.64 
L 359.95476 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.447234 224.64 
L 360.447234 496.44 
L 360.606724 496.44 
L 360.606724 224.64 
L 360.447234 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 360.606724 224.64 
L 360.606724 496.44 
L 361.092908 496.44 
L 361.092908 224.64 
L 360.606724 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.092908 224.64 
L 361.092908 496.44 
L 361.272859 496.44 
L 361.272859 224.64 
L 361.092908 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.272859 224.64 
L 361.272859 496.44 
L 361.486518 496.44 
L 361.486518 224.64 
L 361.272859 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.486518 224.64 
L 361.486518 496.44 
L 361.636114 496.44 
L 361.636114 224.64 
L 361.486518 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.636114 224.64 
L 361.636114 496.44 
L 361.82512 496.44 
L 361.82512 224.64 
L 361.636114 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 361.82554 224.64 
L 361.82554 496.44 
L 362.258058 496.44 
L 362.258058 224.64 
L 361.82554 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 362.258058 224.64 
L 362.258058 496.44 
L 363.145819 496.44 
L 363.145819 224.64 
L 362.258058 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 363.145819 224.64 
L 363.145819 496.44 
L 364.018234 496.44 
L 364.018234 224.64 
L 363.145819 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.018234 224.64 
L 364.018234 496.44 
L 364.388868 496.44 
L 364.388868 224.64 
L 364.018234 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.388868 224.64 
L 364.388868 496.44 
L 364.434569 496.44 
L 364.434569 224.64 
L 364.388868 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.434569 224.64 
L 364.434569 496.44 
L 364.617706 496.44 
L 364.617706 224.64 
L 364.434569 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.617706 224.64 
L 364.617706 496.44 
L 364.634225 496.44 
L 364.634225 224.64 
L 364.617706 224.64 
z
" style="fill:#f7f7fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.634225 224.64 
L 364.634225 496.44 
L 364.705417 496.44 
L 364.705417 224.64 
L 364.634225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.705417 224.64 
L 364.705417 496.44 
L 364.809396 496.44 
L 364.809396 224.64 
L 364.705417 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 364.809396 224.64 
L 364.809396 496.44 
L 365.014502 496.44 
L 365.014502 224.64 
L 364.809396 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.014502 224.64 
L 365.014502 496.44 
L 365.35302 496.44 
L 365.35302 224.64 
L 365.014502 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.35344 224.64 
L 365.35344 496.44 
L 365.363754 496.44 
L 365.363754 224.64 
L 365.35344 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.363754 224.64 
L 365.363754 496.44 
L 365.476369 496.44 
L 365.476369 224.64 
L 365.363754 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.476369 224.64 
L 365.476369 496.44 
L 365.706464 496.44 
L 365.706464 224.64 
L 365.476369 224.64 
z
" style="fill:#dd8585;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.706464 224.64 
L 365.706464 496.44 
L 365.761137 496.44 
L 365.761137 224.64 
L 365.706464 224.64 
z
" style="fill:#e19898;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 365.761137 224.64 
L 365.761137 496.44 
L 366.024774 496.44 
L 366.024774 224.64 
L 365.761137 224.64 
z
" style="fill:#dc8282;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.024774 224.64 
L 366.024774 496.44 
L 366.157598 496.44 
L 366.157598 224.64 
L 366.024774 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.157598 224.64 
L 366.157598 496.44 
L 366.538127 496.44 
L 366.538127 224.64 
L 366.157598 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.538127 224.64 
L 366.538127 496.44 
L 366.691328 496.44 
L 366.691328 224.64 
L 366.538127 224.64 
z
" style="fill:#d35c5c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 366.691328 224.64 
L 366.691328 496.44 
L 367.307235 496.44 
L 367.307235 224.64 
L 366.691328 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.307654 224.64 
L 367.307654 496.44 
L 367.437124 496.44 
L 367.437124 224.64 
L 367.307654 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.437124 224.64 
L 367.437124 496.44 
L 367.503704 496.44 
L 367.503704 224.64 
L 367.437124 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.503704 224.64 
L 367.503704 496.44 
L 367.706127 496.44 
L 367.706127 224.64 
L 367.503704 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.706127 224.64 
L 367.706127 496.44 
L 367.857735 496.44 
L 367.857735 224.64 
L 367.706127 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 367.857735 224.64 
L 367.857735 496.44 
L 368.061836 496.44 
L 368.061836 224.64 
L 367.857735 224.64 
z
" style="fill:#d76f6f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.061836 224.64 
L 368.061836 496.44 
L 368.073743 496.44 
L 368.073743 224.64 
L 368.061836 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.073743 224.64 
L 368.073743 496.44 
L 368.095209 496.44 
L 368.095209 224.64 
L 368.073743 224.64 
z
" style="fill:#db7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.099318 224.64 
L 368.099318 496.44 
L 368.303167 496.44 
L 368.303167 224.64 
L 368.099318 224.64 
z
" style="fill:#dd8686;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.303167 224.64 
L 368.303167 496.44 
L 368.47121 496.44 
L 368.47121 224.64 
L 368.303167 224.64 
z
" style="fill:#d76d6d;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.475571 224.64 
L 368.475571 496.44 
L 368.4884 496.44 
L 368.4884 224.64 
L 368.475571 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.4884 224.64 
L 368.4884 496.44 
L 368.5206 496.44 
L 368.5206 224.64 
L 368.4884 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.523116 224.64 
L 368.523116 496.44 
L 368.644536 496.44 
L 368.644536 224.64 
L 368.523116 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.647387 224.64 
L 368.647387 496.44 
L 368.65833 496.44 
L 368.65833 224.64 
L 368.647387 224.64 
z
" style="fill:#d66b6b;"/>
   </g>
   <g id="BrokenBarHCollection_101">
    <path clip-path="url(#p9901fb19d8)" d="M 368.660049 224.64 
L 368.660049 496.44 
L 368.672082 496.44 
L 368.672082 224.64 
L 368.660049 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.672502 224.64 
L 368.672502 496.44 
L 368.741262 496.44 
L 368.741262 224.64 
L 368.672502 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.741262 224.64 
L 368.741262 496.44 
L 368.863689 496.44 
L 368.863689 224.64 
L 368.741262 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 368.863689 224.64 
L 368.863689 496.44 
L 369.462154 496.44 
L 369.462154 224.64 
L 368.863689 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.462154 224.64 
L 369.462154 496.44 
L 369.720088 496.44 
L 369.720088 224.64 
L 369.462154 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 369.720088 224.64 
L 369.720088 496.44 
L 370.16334 496.44 
L 370.16334 224.64 
L 369.720088 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.16334 224.64 
L 370.16334 496.44 
L 370.809014 496.44 
L 370.809014 224.64 
L 370.16334 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 370.809014 224.64 
L 370.809014 496.44 
L 371.148203 496.44 
L 371.148203 224.64 
L 370.809014 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.148203 224.64 
L 371.148203 496.44 
L 371.311215 496.44 
L 371.311215 224.64 
L 371.148203 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.311634 224.64 
L 371.311634 496.44 
L 371.436157 496.44 
L 371.436157 224.64 
L 371.311634 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.436157 224.64 
L 371.436157 496.44 
L 371.575858 496.44 
L 371.575858 224.64 
L 371.436157 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 371.575858 224.64 
L 371.575858 496.44 
L 372.065145 496.44 
L 372.065145 224.64 
L 371.575858 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 372.065145 224.64 
L 372.065145 496.44 
L 373.241867 496.44 
L 373.241867 224.64 
L 372.065145 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 373.241867 224.64 
L 373.241867 496.44 
L 374.778153 496.44 
L 374.778153 224.64 
L 373.241867 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.778153 224.64 
L 374.778153 496.44 
L 374.812198 496.44 
L 374.812198 224.64 
L 374.778153 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 374.812198 224.64 
L 374.812198 496.44 
L 375.04506 496.44 
L 375.04506 224.64 
L 374.812198 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.04506 224.64 
L 375.04506 496.44 
L 375.177969 496.44 
L 375.177969 224.64 
L 375.04506 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.177969 224.64 
L 375.177969 496.44 
L 375.189121 496.44 
L 375.189121 224.64 
L 375.177969 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.197339 224.64 
L 375.197339 496.44 
L 375.234151 496.44 
L 375.234151 224.64 
L 375.197339 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.245806 224.64 
L 375.245806 496.44 
L 375.272304 496.44 
L 375.272304 224.64 
L 375.245806 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.272723 224.64 
L 375.272723 496.44 
L 375.284966 496.44 
L 375.284966 224.64 
L 375.272723 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.292345 224.64 
L 375.292345 496.44 
L 375.306517 496.44 
L 375.306517 224.64 
L 375.292345 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.306936 224.64 
L 375.306936 496.44 
L 375.353894 496.44 
L 375.353894 224.64 
L 375.306936 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.354733 224.64 
L 375.354733 496.44 
L 375.377373 496.44 
L 375.377373 224.64 
L 375.354733 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.396408 224.64 
L 375.396408 496.44 
L 375.432465 496.44 
L 375.432465 224.64 
L 375.396408 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.432884 224.64 
L 375.432884 496.44 
L 375.509862 496.44 
L 375.509862 224.64 
L 375.432884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.510281 224.64 
L 375.510281 496.44 
L 375.533928 496.44 
L 375.533928 224.64 
L 375.510281 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.549022 224.64 
L 375.549022 496.44 
L 375.585247 496.44 
L 375.585247 224.64 
L 375.549022 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.593465 224.64 
L 375.593465 496.44 
L 375.612751 496.44 
L 375.612751 224.64 
L 375.593465 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.613925 224.64 
L 375.613925 496.44 
L 375.626671 496.44 
L 375.626671 224.64 
L 375.613925 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.629102 224.64 
L 375.629102 496.44 
L 375.658787 496.44 
L 375.658787 224.64 
L 375.629102 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.661805 224.64 
L 375.661805 496.44 
L 375.683775 496.44 
L 375.683775 224.64 
L 375.661805 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.683775 224.64 
L 375.683775 496.44 
L 375.703649 496.44 
L 375.703649 224.64 
L 375.683775 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.703649 224.64 
L 375.703649 496.44 
L 375.726289 496.44 
L 375.726289 224.64 
L 375.703649 224.64 
z
" style="fill:#efcece;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.726289 224.64 
L 375.726289 496.44 
L 375.743898 496.44 
L 375.743898 224.64 
L 375.726289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.744485 224.64 
L 375.744485 496.44 
L 375.755554 496.44 
L 375.755554 224.64 
L 375.744485 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.768216 224.64 
L 375.768216 496.44 
L 375.798906 496.44 
L 375.798906 224.64 
L 375.768216 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.803518 224.64 
L 375.803518 496.44 
L 375.818193 496.44 
L 375.818193 224.64 
L 375.803518 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.818612 224.64 
L 375.818612 496.44 
L 375.845529 496.44 
L 375.845529 224.64 
L 375.818612 224.64 
z
" style="fill:#f1d6d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.847626 224.64 
L 375.847626 496.44 
L 375.867164 496.44 
L 375.867164 224.64 
L 375.847626 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.875214 224.64 
L 375.875214 496.44 
L 375.930054 496.44 
L 375.930054 224.64 
L 375.875214 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 375.930892 224.64 
L 375.930892 496.44 
L 376.026318 496.44 
L 376.026318 224.64 
L 375.930892 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.026737 224.64 
L 376.026737 496.44 
L 376.046443 496.44 
L 376.046443 224.64 
L 376.026737 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.046862 224.64 
L 376.046862 496.44 
L 376.078308 496.44 
L 376.078308 224.64 
L 376.046862 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.083423 224.64 
L 376.083423 496.44 
L 376.097929 496.44 
L 376.097929 224.64 
L 376.083423 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.097929 224.64 
L 376.097929 496.44 
L 376.113442 496.44 
L 376.113442 224.64 
L 376.097929 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.113442 224.64 
L 376.113442 496.44 
L 376.144888 496.44 
L 376.144888 224.64 
L 376.113442 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.14581 224.64 
L 376.14581 496.44 
L 376.162245 496.44 
L 376.162245 224.64 
L 376.14581 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.176752 224.64 
L 376.176752 496.44 
L 376.199225 496.44 
L 376.199225 224.64 
L 376.176752 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.217757 224.64 
L 376.217757 496.44 
L 376.226813 496.44 
L 376.226813 224.64 
L 376.217757 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.233773 224.64 
L 376.233773 496.44 
L 376.359973 496.44 
L 376.359973 224.64 
L 376.233773 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.361231 224.64 
L 376.361231 496.44 
L 376.374479 496.44 
L 376.374479 224.64 
L 376.361231 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.388399 224.64 
L 376.388399 496.44 
L 376.404583 496.44 
L 376.404583 224.64 
L 376.388399 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.406512 224.64 
L 376.406512 496.44 
L 376.418167 496.44 
L 376.418167 224.64 
L 376.406512 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.419006 224.64 
L 376.419006 496.44 
L 376.436951 496.44 
L 376.436951 224.64 
L 376.419006 224.64 
z
" style="fill:#f5e2e2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.437957 224.64 
L 376.437957 496.44 
L 376.505375 496.44 
L 376.505375 224.64 
L 376.437957 224.64 
z
" style="fill:#f3dcdc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.505375 224.64 
L 376.505375 496.44 
L 376.52592 496.44 
L 376.52592 224.64 
L 376.505375 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 376.53833 224.64 
L 376.53833 496.44 
L 378.115831 496.44 
L 378.115831 224.64 
L 376.53833 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 378.115831 224.64 
L 378.115831 496.44 
L 379.642432 496.44 
L 379.642432 224.64 
L 378.115831 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.644613 224.64 
L 379.644613 496.44 
L 379.667253 496.44 
L 379.667253 224.64 
L 379.644613 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.667253 224.64 
L 379.667253 496.44 
L 379.684359 496.44 
L 379.684359 224.64 
L 379.667253 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.703897 224.64 
L 379.703897 496.44 
L 379.727209 496.44 
L 379.727209 224.64 
L 379.703897 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.727712 224.64 
L 379.727712 496.44 
L 379.742135 496.44 
L 379.742135 224.64 
L 379.727712 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.758738 224.64 
L 379.758738 496.44 
L 379.794208 496.44 
L 379.794208 224.64 
L 379.758738 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.794627 224.64 
L 379.794627 496.44 
L 379.825569 496.44 
L 379.825569 224.64 
L 379.794627 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.825569 224.64 
L 379.825569 496.44 
L 379.881416 496.44 
L 379.881416 224.64 
L 379.825569 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.904979 224.64 
L 379.904979 496.44 
L 379.985311 496.44 
L 379.985311 224.64 
L 379.904979 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.985311 224.64 
L 379.985311 496.44 
L 379.996547 496.44 
L 379.996547 224.64 
L 379.985311 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 379.996967 224.64 
L 379.996967 496.44 
L 380.007616 496.44 
L 380.007616 224.64 
L 379.996967 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.014995 224.64 
L 380.014995 496.44 
L 380.027992 496.44 
L 380.027992 224.64 
L 380.014995 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.033108 224.64 
L 380.033108 496.44 
L 380.236034 496.44 
L 380.236034 224.64 
L 380.033108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.236034 224.64 
L 380.236034 496.44 
L 380.352507 496.44 
L 380.352507 224.64 
L 380.236034 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.353345 224.64 
L 380.353345 496.44 
L 380.403867 496.44 
L 380.403867 224.64 
L 380.353345 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.403867 224.64 
L 380.403867 496.44 
L 380.412379 496.44 
L 380.412379 224.64 
L 380.403867 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.430659 224.64 
L 380.430659 496.44 
L 380.480887 496.44 
L 380.480887 224.64 
L 380.430659 224.64 
z
" style="fill:#f0d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.480887 224.64 
L 380.480887 496.44 
L 380.511158 496.44 
L 380.511158 224.64 
L 380.480887 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.511158 224.64 
L 380.511158 496.44 
L 380.652452 496.44 
L 380.652452 224.64 
L 380.511158 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.652452 224.64 
L 380.652452 496.44 
L 380.952649 496.44 
L 380.952649 224.64 
L 380.652452 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 380.952649 224.64 
L 380.952649 496.44 
L 381.280769 496.44 
L 381.280769 224.64 
L 380.952649 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.280769 224.64 
L 381.280769 496.44 
L 381.606038 496.44 
L 381.606038 224.64 
L 381.280769 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.606038 224.64 
L 381.606038 496.44 
L 381.89634 496.44 
L 381.89634 224.64 
L 381.606038 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 381.89634 224.64 
L 381.89634 496.44 
L 382.124591 496.44 
L 382.124591 224.64 
L 381.89634 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.124591 224.64 
L 382.124591 496.44 
L 382.379171 496.44 
L 382.379171 224.64 
L 382.124591 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.379171 224.64 
L 382.379171 496.44 
L 382.698738 496.44 
L 382.698738 224.64 
L 382.379171 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.698738 224.64 
L 382.698738 496.44 
L 382.78385 496.44 
L 382.78385 224.64 
L 382.698738 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.78385 224.64 
L 382.78385 496.44 
L 382.833994 496.44 
L 382.833994 224.64 
L 382.78385 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 382.833994 224.64 
L 382.833994 496.44 
L 383.436233 496.44 
L 383.436233 224.64 
L 382.833994 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.436233 224.64 
L 383.436233 496.44 
L 383.625072 496.44 
L 383.625072 224.64 
L 383.436233 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.625072 224.64 
L 383.625072 496.44 
L 383.662135 496.44 
L 383.662135 224.64 
L 383.625072 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.662135 224.64 
L 383.662135 496.44 
L 383.878897 496.44 
L 383.878897 224.64 
L 383.662135 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.878897 224.64 
L 383.878897 496.44 
L 383.965686 496.44 
L 383.965686 224.64 
L 383.878897 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 383.965686 224.64 
L 383.965686 496.44 
L 384.075703 496.44 
L 384.075703 224.64 
L 383.965686 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.075703 224.64 
L 384.075703 496.44 
L 384.174566 496.44 
L 384.174566 224.64 
L 384.075703 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.174566 224.64 
L 384.174566 496.44 
L 384.346886 496.44 
L 384.346886 224.64 
L 384.174566 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.346886 224.64 
L 384.346886 496.44 
L 384.752655 496.44 
L 384.752655 224.64 
L 384.346886 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.752655 224.64 
L 384.752655 496.44 
L 384.887995 496.44 
L 384.887995 224.64 
L 384.752655 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 384.887995 224.64 
L 384.887995 496.44 
L 385.40051 496.44 
L 385.40051 224.64 
L 384.887995 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.40051 224.64 
L 385.40051 496.44 
L 385.915876 496.44 
L 385.915876 224.64 
L 385.40051 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 385.915876 224.64 
L 385.915876 496.44 
L 386.048365 496.44 
L 386.048365 224.64 
L 385.915876 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.048365 224.64 
L 386.048365 496.44 
L 386.3977 496.44 
L 386.3977 224.64 
L 386.048365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.398119 224.64 
L 386.398119 496.44 
L 386.748041 496.44 
L 386.748041 224.64 
L 386.398119 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 386.748041 224.64 
L 386.748041 496.44 
L 387.041195 496.44 
L 387.041195 224.64 
L 386.748041 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.041195 224.64 
L 387.041195 496.44 
L 387.125552 496.44 
L 387.125552 224.64 
L 387.041195 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.125552 224.64 
L 387.125552 496.44 
L 387.167478 496.44 
L 387.167478 224.64 
L 387.125552 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.167478 224.64 
L 387.167478 496.44 
L 387.319254 496.44 
L 387.319254 224.64 
L 387.167478 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.319254 224.64 
L 387.319254 496.44 
L 387.841999 496.44 
L 387.841999 224.64 
L 387.319254 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 387.841999 224.64 
L 387.841999 496.44 
L 388.445579 496.44 
L 388.445579 224.64 
L 387.841999 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.445579 224.64 
L 388.445579 496.44 
L 388.614125 496.44 
L 388.614125 224.64 
L 388.445579 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.614125 224.64 
L 388.614125 496.44 
L 388.789883 496.44 
L 388.789883 224.64 
L 388.614125 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 388.789883 224.64 
L 388.789883 496.44 
L 389.02895 496.44 
L 389.02895 224.64 
L 388.789883 224.64 
z
" style="fill:#fbf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.02895 224.64 
L 389.02895 496.44 
L 389.374345 496.44 
L 389.374345 224.64 
L 389.02895 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.374345 224.64 
L 389.374345 496.44 
L 389.474969 496.44 
L 389.474969 224.64 
L 389.374345 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 389.474969 224.64 
L 389.474969 496.44 
L 390.415977 496.44 
L 390.415977 224.64 
L 389.474969 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.415977 224.64 
L 390.415977 496.44 
L 390.468554 496.44 
L 390.468554 224.64 
L 390.415977 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.468554 224.64 
L 390.468554 496.44 
L 390.904091 496.44 
L 390.904091 224.64 
L 390.468554 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 390.904091 224.64 
L 390.904091 496.44 
L 391.085886 496.44 
L 391.085886 224.64 
L 390.904091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.085886 224.64 
L 391.085886 496.44 
L 391.631188 496.44 
L 391.631188 224.64 
L 391.085886 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.631607 224.64 
L 391.631607 496.44 
L 391.685944 496.44 
L 391.685944 224.64 
L 391.631607 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.685944 224.64 
L 391.685944 496.44 
L 391.77986 496.44 
L 391.77986 224.64 
L 391.685944 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.77986 224.64 
L 391.77986 496.44 
L 391.926521 496.44 
L 391.926521 224.64 
L 391.77986 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 391.926521 224.64 
L 391.926521 496.44 
L 392.161815 496.44 
L 392.161815 224.64 
L 391.926521 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.161815 224.64 
L 392.161815 496.44 
L 392.330738 496.44 
L 392.330738 224.64 
L 392.161815 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_102">
    <path clip-path="url(#p9901fb19d8)" d="M 392.340843 224.64 
L 392.340843 496.44 
L 392.785898 496.44 
L 392.785898 224.64 
L 392.340843 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.785898 224.64 
L 392.785898 496.44 
L 392.901784 496.44 
L 392.901784 224.64 
L 392.785898 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 392.901784 224.64 
L 392.901784 496.44 
L 393.021359 496.44 
L 393.021359 224.64 
L 392.901784 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.021359 224.64 
L 393.021359 496.44 
L 393.483981 496.44 
L 393.483981 224.64 
L 393.021359 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.484568 224.64 
L 393.484568 496.44 
L 393.595339 496.44 
L 393.595339 224.64 
L 393.484568 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.595339 224.64 
L 393.595339 496.44 
L 393.782585 496.44 
L 393.782585 224.64 
L 393.595339 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 393.782585 224.64 
L 393.782585 496.44 
L 394.181813 496.44 
L 394.181813 224.64 
L 393.782585 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.181813 224.64 
L 394.181813 496.44 
L 394.285624 496.44 
L 394.285624 224.64 
L 394.181813 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.285624 224.64 
L 394.285624 496.44 
L 394.492827 496.44 
L 394.492827 224.64 
L 394.285624 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.492827 224.64 
L 394.492827 496.44 
L 394.584563 496.44 
L 394.584563 224.64 
L 394.492827 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.584563 224.64 
L 394.584563 496.44 
L 394.727031 496.44 
L 394.727031 224.64 
L 394.584563 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.727031 224.64 
L 394.727031 496.44 
L 394.895996 496.44 
L 394.895996 224.64 
L 394.727031 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.895996 224.64 
L 394.895996 496.44 
L 394.947483 496.44 
L 394.947483 224.64 
L 394.895996 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 394.947483 224.64 
L 394.947483 496.44 
L 395.119635 496.44 
L 395.119635 224.64 
L 394.947483 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.119635 224.64 
L 395.119635 496.44 
L 395.25095 496.44 
L 395.25095 224.64 
L 395.119635 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.25095 224.64 
L 395.25095 496.44 
L 395.318704 496.44 
L 395.318704 224.64 
L 395.25095 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.31971 224.64 
L 395.31971 496.44 
L 395.34126 496.44 
L 395.34126 224.64 
L 395.31971 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.342183 224.64 
L 395.342183 496.44 
L 395.356354 496.44 
L 395.356354 224.64 
L 395.342183 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.367674 224.64 
L 395.367674 496.44 
L 395.380001 496.44 
L 395.380001 224.64 
L 395.367674 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.384864 224.64 
L 395.384864 496.44 
L 395.523056 496.44 
L 395.523056 224.64 
L 395.384864 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.523056 224.64 
L 395.523056 496.44 
L 395.782499 496.44 
L 395.782499 224.64 
L 395.523056 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.788369 224.64 
L 395.788369 496.44 
L 395.9383 496.44 
L 395.9383 224.64 
L 395.788369 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.9383 224.64 
L 395.9383 496.44 
L 395.986767 496.44 
L 395.986767 224.64 
L 395.9383 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 395.986767 224.64 
L 395.986767 496.44 
L 396.062739 496.44 
L 396.062739 224.64 
L 395.986767 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.062739 224.64 
L 396.062739 496.44 
L 396.18961 496.44 
L 396.18961 224.64 
L 396.062739 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.18961 224.64 
L 396.18961 496.44 
L 396.434128 496.44 
L 396.434128 224.64 
L 396.18961 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.434128 224.64 
L 396.434128 496.44 
L 396.600578 496.44 
L 396.600578 224.64 
L 396.434128 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.600578 224.64 
L 396.600578 496.44 
L 396.766692 496.44 
L 396.766692 224.64 
L 396.600578 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 396.766692 224.64 
L 396.766692 496.44 
L 397.183027 496.44 
L 397.183027 224.64 
L 396.766692 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.183027 224.64 
L 397.183027 496.44 
L 397.502091 496.44 
L 397.502091 224.64 
L 397.183027 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.502091 224.64 
L 397.502091 496.44 
L 397.737804 496.44 
L 397.737804 224.64 
L 397.502091 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.737804 224.64 
L 397.737804 496.44 
L 397.902241 496.44 
L 397.902241 224.64 
L 397.737804 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 397.902241 224.64 
L 397.902241 496.44 
L 398.270108 496.44 
L 398.270108 224.64 
L 397.902241 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.270108 224.64 
L 398.270108 496.44 
L 398.352788 496.44 
L 398.352788 224.64 
L 398.270108 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.352788 224.64 
L 398.352788 496.44 
L 398.597138 496.44 
L 398.597138 224.64 
L 398.352788 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.597138 224.64 
L 398.597138 496.44 
L 398.8326 496.44 
L 398.8326 224.64 
L 398.597138 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.8326 224.64 
L 398.8326 496.44 
L 398.851635 496.44 
L 398.851635 224.64 
L 398.8326 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.851635 224.64 
L 398.851635 496.44 
L 398.884589 496.44 
L 398.884589 224.64 
L 398.851635 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 398.884589 224.64 
L 398.884589 496.44 
L 399.165626 496.44 
L 399.165626 224.64 
L 398.884589 224.64 
z
" style="fill:#f8f8fc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.165626 224.64 
L 399.165626 496.44 
L 399.439786 496.44 
L 399.439786 224.64 
L 399.165626 224.64 
z
" style="fill:#e3e3f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.439786 224.64 
L 399.439786 496.44 
L 399.511649 496.44 
L 399.511649 224.64 
L 399.439786 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.511649 224.64 
L 399.511649 496.44 
L 399.68271 496.44 
L 399.68271 224.64 
L 399.511649 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.68271 224.64 
L 399.68271 496.44 
L 399.915489 496.44 
L 399.915489 224.64 
L 399.68271 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 399.915489 224.64 
L 399.915489 496.44 
L 400.105502 496.44 
L 400.105502 224.64 
L 399.915489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.105502 224.64 
L 400.105502 496.44 
L 400.129819 496.44 
L 400.129819 224.64 
L 400.105502 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.182815 224.64 
L 400.182815 496.44 
L 400.195225 496.44 
L 400.195225 224.64 
L 400.182815 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.195225 224.64 
L 400.195225 496.44 
L 400.239752 496.44 
L 400.239752 224.64 
L 400.195225 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.240171 224.64 
L 400.240171 496.44 
L 400.264489 496.44 
L 400.264489 224.64 
L 400.240171 224.64 
z
" style="fill:#f5e4e4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.264489 224.64 
L 400.264489 496.44 
L 400.283104 496.44 
L 400.283104 224.64 
L 400.264489 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.283104 224.64 
L 400.283104 496.44 
L 400.414922 496.44 
L 400.414922 224.64 
L 400.283104 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.430939 224.64 
L 400.430939 496.44 
L 400.548753 496.44 
L 400.548753 224.64 
L 400.430939 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.552527 224.64 
L 400.552527 496.44 
L 400.607032 496.44 
L 400.607032 224.64 
L 400.552527 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.607451 224.64 
L 400.607451 496.44 
L 400.816331 496.44 
L 400.816331 224.64 
L 400.607451 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.816331 224.64 
L 400.816331 496.44 
L 400.925844 496.44 
L 400.925844 224.64 
L 400.816331 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.926515 224.64 
L 400.926515 496.44 
L 400.948233 496.44 
L 400.948233 224.64 
L 400.926515 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.948904 224.64 
L 400.948904 496.44 
L 400.98647 496.44 
L 400.98647 224.64 
L 400.948904 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 400.987309 224.64 
L 400.987309 496.44 
L 401.005673 496.44 
L 401.005673 224.64 
L 400.987309 224.64 
z
" style="fill:#f0d3d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.005673 224.64 
L 401.005673 496.44 
L 401.036615 496.44 
L 401.036615 224.64 
L 401.005673 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.045168 224.64 
L 401.045168 496.44 
L 401.369096 496.44 
L 401.369096 224.64 
L 401.045168 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.369096 224.64 
L 401.369096 496.44 
L 401.486407 496.44 
L 401.486407 224.64 
L 401.369096 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 401.486826 224.64 
L 401.486826 496.44 
L 402.264068 496.44 
L 402.264068 224.64 
L 401.486826 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.264487 224.64 
L 402.264487 496.44 
L 402.457351 496.44 
L 402.457351 224.64 
L 402.264487 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.457351 224.64 
L 402.457351 496.44 
L 402.631516 496.44 
L 402.631516 224.64 
L 402.457351 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.631516 224.64 
L 402.631516 496.44 
L 402.838383 496.44 
L 402.838383 224.64 
L 402.631516 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 402.838383 224.64 
L 402.838383 496.44 
L 403.014979 496.44 
L 403.014979 224.64 
L 402.838383 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.014979 224.64 
L 403.014979 496.44 
L 403.194594 496.44 
L 403.194594 224.64 
L 403.014979 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.194594 224.64 
L 403.194594 496.44 
L 403.467203 496.44 
L 403.467203 224.64 
L 403.194594 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.467203 224.64 
L 403.467203 496.44 
L 403.672981 496.44 
L 403.672981 224.64 
L 403.467203 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.672981 224.64 
L 403.672981 496.44 
L 403.983995 496.44 
L 403.983995 224.64 
L 403.672981 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 403.984414 224.64 
L 403.984414 496.44 
L 404.235137 496.44 
L 404.235137 224.64 
L 403.984414 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.235137 224.64 
L 404.235137 496.44 
L 404.626818 496.44 
L 404.626818 224.64 
L 404.235137 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.626818 224.64 
L 404.626818 496.44 
L 404.674615 496.44 
L 404.674615 224.64 
L 404.626818 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 404.674615 224.64 
L 404.674615 496.44 
L 405.224109 496.44 
L 405.224109 224.64 
L 404.674615 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.224109 224.64 
L 405.224109 496.44 
L 405.709875 496.44 
L 405.709875 224.64 
L 405.224109 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 405.709875 224.64 
L 405.709875 496.44 
L 406.04202 496.44 
L 406.04202 224.64 
L 405.709875 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.04202 224.64 
L 406.04202 496.44 
L 406.940682 496.44 
L 406.940682 224.64 
L 406.04202 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 406.941437 224.64 
L 406.941437 496.44 
L 407.110738 496.44 
L 407.110738 224.64 
L 406.941437 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.110738 224.64 
L 407.110738 496.44 
L 407.262262 496.44 
L 407.262262 224.64 
L 407.110738 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.262262 224.64 
L 407.262262 496.44 
L 407.629038 496.44 
L 407.629038 224.64 
L 407.262262 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.629038 224.64 
L 407.629038 496.44 
L 407.940052 496.44 
L 407.940052 224.64 
L 407.629038 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 407.940052 224.64 
L 407.940052 496.44 
L 408.413911 496.44 
L 408.413911 224.64 
L 407.940052 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.413911 224.64 
L 408.413911 496.44 
L 408.504808 496.44 
L 408.504808 224.64 
L 408.413911 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.504808 224.64 
L 408.504808 496.44 
L 408.623713 496.44 
L 408.623713 224.64 
L 408.504808 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.623713 224.64 
L 408.623713 496.44 
L 408.848525 496.44 
L 408.848525 224.64 
L 408.623713 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 408.848525 224.64 
L 408.848525 496.44 
L 409.122057 496.44 
L 409.122057 224.64 
L 408.848525 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.122057 224.64 
L 409.122057 496.44 
L 409.313327 496.44 
L 409.313327 224.64 
L 409.122057 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.313327 224.64 
L 409.313327 496.44 
L 409.992963 496.44 
L 409.992963 224.64 
L 409.313327 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 409.992963 224.64 
L 409.992963 496.44 
L 410.153627 496.44 
L 410.153627 224.64 
L 409.992963 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.153627 224.64 
L 410.153627 496.44 
L 410.615662 496.44 
L 410.615662 224.64 
L 410.153627 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 410.615662 224.64 
L 410.615662 496.44 
L 411.042897 496.44 
L 411.042897 224.64 
L 410.615662 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.043316 224.64 
L 411.043316 496.44 
L 411.28079 496.44 
L 411.28079 224.64 
L 411.043316 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 411.28079 224.64 
L 411.28079 496.44 
L 412.112453 496.44 
L 412.112453 224.64 
L 411.28079 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.112453 224.64 
L 412.112453 496.44 
L 412.280999 496.44 
L 412.280999 224.64 
L 412.112453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.280999 224.64 
L 412.280999 496.44 
L 412.727773 496.44 
L 412.727773 224.64 
L 412.280999 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.727773 224.64 
L 412.727773 496.44 
L 412.862945 496.44 
L 412.862945 224.64 
L 412.727773 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 412.862945 224.64 
L 412.862945 496.44 
L 413.18704 496.44 
L 413.18704 224.64 
L 412.862945 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.18704 224.64 
L 413.18704 496.44 
L 413.404222 496.44 
L 413.404222 224.64 
L 413.18704 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.404222 224.64 
L 413.404222 496.44 
L 413.537214 496.44 
L 413.537214 224.64 
L 413.404222 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.537214 224.64 
L 413.537214 496.44 
L 413.565138 496.44 
L 413.565138 224.64 
L 413.537214 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.565138 224.64 
L 413.565138 496.44 
L 413.723286 496.44 
L 413.723286 224.64 
L 413.565138 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.723286 224.64 
L 413.723286 496.44 
L 413.988432 496.44 
L 413.988432 224.64 
L 413.723286 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 413.988432 224.64 
L 413.988432 496.44 
L 414.118322 496.44 
L 414.118322 224.64 
L 413.988432 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.118322 224.64 
L 414.118322 496.44 
L 414.523 496.44 
L 414.523 224.64 
L 414.118322 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.523 224.64 
L 414.523 496.44 
L 414.59872 496.44 
L 414.59872 224.64 
L 414.523 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.59914 224.64 
L 414.59914 496.44 
L 414.717374 496.44 
L 414.717374 224.64 
L 414.59914 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.717374 224.64 
L 414.717374 496.44 
L 414.788901 496.44 
L 414.788901 224.64 
L 414.717374 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.788901 224.64 
L 414.788901 496.44 
L 414.948056 496.44 
L 414.948056 224.64 
L 414.788901 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 414.948056 224.64 
L 414.948056 496.44 
L 415.053208 496.44 
L 415.053208 224.64 
L 414.948056 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_103">
    <path clip-path="url(#p9901fb19d8)" d="M 415.071237 224.64 
L 415.071237 496.44 
L 415.295714 496.44 
L 415.295714 224.64 
L 415.071237 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.295714 224.64 
L 415.295714 496.44 
L 415.627691 496.44 
L 415.627691 224.64 
L 415.295714 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 415.627691 224.64 
L 415.627691 496.44 
L 416.01627 496.44 
L 416.01627 224.64 
L 415.627691 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.01627 224.64 
L 416.01627 496.44 
L 416.174586 496.44 
L 416.174586 224.64 
L 416.01627 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.174586 224.64 
L 416.174586 496.44 
L 416.783785 496.44 
L 416.783785 224.64 
L 416.174586 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.783785 224.64 
L 416.783785 496.44 
L 416.863697 496.44 
L 416.863697 224.64 
L 416.783785 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 416.863697 224.64 
L 416.863697 496.44 
L 417.115259 496.44 
L 417.115259 224.64 
L 416.863697 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.115259 224.64 
L 417.115259 496.44 
L 417.234835 496.44 
L 417.234835 224.64 
L 417.115259 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.234835 224.64 
L 417.234835 496.44 
L 417.815103 496.44 
L 417.815103 224.64 
L 417.234835 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 417.815103 224.64 
L 417.815103 496.44 
L 418.803321 496.44 
L 418.803321 224.64 
L 417.815103 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 418.803321 224.64 
L 418.803321 496.44 
L 420.047377 496.44 
L 420.047377 224.64 
L 418.803321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.047377 224.64 
L 420.047377 496.44 
L 420.643159 496.44 
L 420.643159 224.64 
L 420.047377 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.643159 224.64 
L 420.643159 496.44 
L 420.990482 496.44 
L 420.990482 224.64 
L 420.643159 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 420.990482 224.64 
L 420.990482 496.44 
L 421.132866 496.44 
L 421.132866 224.64 
L 420.990482 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.132866 224.64 
L 421.132866 496.44 
L 421.386524 496.44 
L 421.386524 224.64 
L 421.132866 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.386943 224.64 
L 421.386943 496.44 
L 421.626513 496.44 
L 421.626513 224.64 
L 421.386943 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 421.626513 224.64 
L 421.626513 496.44 
L 422.33055 496.44 
L 422.33055 224.64 
L 421.626513 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.33055 224.64 
L 422.33055 496.44 
L 422.847174 496.44 
L 422.847174 224.64 
L 422.33055 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 422.847174 224.64 
L 422.847174 496.44 
L 423.217053 496.44 
L 423.217053 224.64 
L 422.847174 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.217053 224.64 
L 423.217053 496.44 
L 423.267617 496.44 
L 423.267617 224.64 
L 423.217053 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.267617 224.64 
L 423.267617 496.44 
L 423.461236 496.44 
L 423.461236 224.64 
L 423.267617 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.461655 224.64 
L 423.461655 496.44 
L 423.550456 496.44 
L 423.550456 224.64 
L 423.461655 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.550456 224.64 
L 423.550456 496.44 
L 423.6219 496.44 
L 423.6219 224.64 
L 423.550456 224.64 
z
" style="fill:#fcfcfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.628776 224.64 
L 423.628776 496.44 
L 423.96591 496.44 
L 423.96591 224.64 
L 423.628776 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 423.96591 224.64 
L 423.96591 496.44 
L 424.240658 496.44 
L 424.240658 224.64 
L 423.96591 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.241077 224.64 
L 424.241077 496.44 
L 424.282249 496.44 
L 424.282249 224.64 
L 424.241077 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.282249 224.64 
L 424.282249 496.44 
L 424.840045 496.44 
L 424.840045 224.64 
L 424.282249 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.840045 224.64 
L 424.840045 496.44 
L 424.990479 496.44 
L 424.990479 224.64 
L 424.840045 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 424.990479 224.64 
L 424.990479 496.44 
L 425.223844 496.44 
L 425.223844 224.64 
L 424.990479 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.223844 224.64 
L 425.223844 496.44 
L 425.456706 496.44 
L 425.456706 224.64 
L 425.223844 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.456706 224.64 
L 425.456706 496.44 
L 425.728728 496.44 
L 425.728728 224.64 
L 425.456706 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 425.728728 224.64 
L 425.728728 496.44 
L 426.652211 496.44 
L 426.652211 224.64 
L 425.728728 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.652211 224.64 
L 426.652211 496.44 
L 426.978319 496.44 
L 426.978319 224.64 
L 426.652211 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 426.978319 224.64 
L 426.978319 496.44 
L 427.331092 496.44 
L 427.331092 224.64 
L 426.978319 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 427.331092 224.64 
L 427.331092 496.44 
L 428.215918 496.44 
L 428.215918 224.64 
L 427.331092 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.215918 224.64 
L 428.215918 496.44 
L 428.523829 496.44 
L 428.523829 224.64 
L 428.215918 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 428.523829 224.64 
L 428.523829 496.44 
L 429.478925 496.44 
L 429.478925 224.64 
L 428.523829 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.479344 224.64 
L 429.479344 496.44 
L 429.728222 496.44 
L 429.728222 224.64 
L 429.479344 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 429.728222 224.64 
L 429.728222 496.44 
L 430.087452 496.44 
L 430.087452 224.64 
L 429.728222 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.10263 224.64 
L 430.10263 496.44 
L 430.154284 496.44 
L 430.154284 224.64 
L 430.10263 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.154284 224.64 
L 430.154284 496.44 
L 430.429492 496.44 
L 430.429492 224.64 
L 430.154284 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.429492 224.64 
L 430.429492 496.44 
L 430.610281 496.44 
L 430.610281 224.64 
L 430.429492 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.610281 224.64 
L 430.610281 496.44 
L 430.876937 496.44 
L 430.876937 224.64 
L 430.610281 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 430.876937 224.64 
L 430.876937 496.44 
L 431.046741 496.44 
L 431.046741 224.64 
L 430.876937 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.04716 224.64 
L 431.04716 496.44 
L 431.874881 496.44 
L 431.874881 224.64 
L 431.04716 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 431.874881 224.64 
L 431.874881 496.44 
L 432.52173 496.44 
L 432.52173 224.64 
L 431.874881 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.52173 224.64 
L 432.52173 496.44 
L 432.926409 496.44 
L 432.926409 224.64 
L 432.52173 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 432.926409 224.64 
L 432.926409 496.44 
L 433.078604 496.44 
L 433.078604 224.64 
L 432.926409 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.078604 224.64 
L 433.078604 496.44 
L 433.1586 496.44 
L 433.1586 224.64 
L 433.078604 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.1586 224.64 
L 433.1586 496.44 
L 433.750022 496.44 
L 433.750022 224.64 
L 433.1586 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 433.750022 224.64 
L 433.750022 496.44 
L 434.347061 496.44 
L 434.347061 224.64 
L 433.750022 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.347061 224.64 
L 434.347061 496.44 
L 434.584451 496.44 
L 434.584451 224.64 
L 434.347061 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 434.584451 224.64 
L 434.584451 496.44 
L 435.14904 496.44 
L 435.14904 224.64 
L 434.584451 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.14904 224.64 
L 435.14904 496.44 
L 435.316663 496.44 
L 435.316663 224.64 
L 435.14904 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.316663 224.64 
L 435.316663 496.44 
L 435.494685 496.44 
L 435.494685 224.64 
L 435.316663 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.495104 224.64 
L 435.495104 496.44 
L 435.949089 496.44 
L 435.949089 224.64 
L 435.495104 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 435.949089 224.64 
L 435.949089 496.44 
L 436.066988 496.44 
L 436.066988 224.64 
L 435.949089 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.066988 224.64 
L 436.066988 496.44 
L 436.274107 496.44 
L 436.274107 224.64 
L 436.066988 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.274107 224.64 
L 436.274107 496.44 
L 436.547303 496.44 
L 436.547303 224.64 
L 436.274107 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.547303 224.64 
L 436.547303 496.44 
L 436.621262 496.44 
L 436.621262 224.64 
L 436.547303 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 436.621262 224.64 
L 436.621262 496.44 
L 437.045479 496.44 
L 437.045479 224.64 
L 436.621262 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.045898 224.64 
L 437.045898 496.44 
L 437.684739 496.44 
L 437.684739 224.64 
L 437.045898 224.64 
z
" style="fill:#fdfcfc;"/>
   </g>
   <g id="BrokenBarHCollection_104">
    <path clip-path="url(#p9901fb19d8)" d="M 437.694843 224.64 
L 437.694843 496.44 
L 437.70499 496.44 
L 437.70499 224.64 
L 437.694843 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.70499 224.64 
L 437.70499 496.44 
L 437.920452 496.44 
L 437.920452 224.64 
L 437.70499 224.64 
z
" style="fill:#d97878;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 437.920452 224.64 
L 437.920452 496.44 
L 438.169834 496.44 
L 438.169834 224.64 
L 437.920452 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.169834 224.64 
L 438.169834 496.44 
L 438.226519 496.44 
L 438.226519 224.64 
L 438.169834 224.64 
z
" style="fill:#dd8888;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.226519 224.64 
L 438.226519 496.44 
L 438.474894 496.44 
L 438.474894 224.64 
L 438.226519 224.64 
z
" style="fill:#d66969;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.474894 224.64 
L 438.474894 496.44 
L 438.745071 496.44 
L 438.745071 224.64 
L 438.474894 224.64 
z
" style="fill:#db8080;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.746916 224.64 
L 438.746916 496.44 
L 438.917139 496.44 
L 438.917139 224.64 
L 438.746916 224.64 
z
" style="fill:#d66767;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.917558 224.64 
L 438.917558 496.44 
L 438.987828 496.44 
L 438.987828 224.64 
L 438.917558 224.64 
z
" style="fill:#d66868;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 438.987828 224.64 
L 438.987828 496.44 
L 439.054492 496.44 
L 439.054492 224.64 
L 438.987828 224.64 
z
" style="fill:#dc8383;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.054492 224.64 
L 439.054492 496.44 
L 439.120066 496.44 
L 439.120066 224.64 
L 439.054492 224.64 
z
" style="fill:#d56565;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.125684 224.64 
L 439.125684 496.44 
L 439.300268 496.44 
L 439.300268 224.64 
L 439.125684 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.317038 224.64 
L 439.317038 496.44 
L 439.458416 496.44 
L 439.458416 224.64 
L 439.317038 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.461938 224.64 
L 439.461938 496.44 
L 439.6143 496.44 
L 439.6143 224.64 
L 439.461938 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.621009 224.64 
L 439.621009 496.44 
L 439.956508 496.44 
L 439.956508 224.64 
L 439.621009 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 439.957011 224.64 
L 439.957011 496.44 
L 440.114405 496.44 
L 440.114405 224.64 
L 439.957011 224.64 
z
" style="fill:#d97474;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.114405 224.64 
L 440.114405 496.44 
L 440.277417 496.44 
L 440.277417 224.64 
L 440.114405 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.277417 224.64 
L 440.277417 496.44 
L 440.851229 496.44 
L 440.851229 224.64 
L 440.277417 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.851229 224.64 
L 440.851229 496.44 
L 440.952943 496.44 
L 440.952943 224.64 
L 440.851229 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.952943 224.64 
L 440.952943 496.44 
L 440.993026 496.44 
L 440.993026 224.64 
L 440.952943 224.64 
z
" style="fill:#e29b9b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 440.993026 224.64 
L 440.993026 496.44 
L 441.152767 496.44 
L 441.152767 224.64 
L 440.993026 224.64 
z
" style="fill:#da7b7b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.152767 224.64 
L 441.152767 496.44 
L 441.47007 496.44 
L 441.47007 224.64 
L 441.152767 224.64 
z
" style="fill:#d76e6e;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.472754 224.64 
L 441.472754 496.44 
L 441.736893 496.44 
L 441.736893 224.64 
L 441.472754 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 441.736893 224.64 
L 441.736893 496.44 
L 442.169495 496.44 
L 442.169495 224.64 
L 441.736893 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.169495 224.64 
L 442.169495 496.44 
L 442.316827 496.44 
L 442.316827 224.64 
L 442.169495 224.64 
z
" style="fill:#d46060;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.316827 224.64 
L 442.316827 496.44 
L 442.547089 496.44 
L 442.547089 224.64 
L 442.316827 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.547089 224.64 
L 442.547089 496.44 
L 442.928121 496.44 
L 442.928121 224.64 
L 442.547089 224.64 
z
" style="fill:#d76c6c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 442.928121 224.64 
L 442.928121 496.44 
L 443.017593 496.44 
L 443.017593 224.64 
L 442.928121 224.64 
z
" style="fill:#db8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.017593 224.64 
L 443.017593 496.44 
L 443.268987 496.44 
L 443.268987 224.64 
L 443.017593 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.27058 224.64 
L 443.27058 496.44 
L 443.44181 496.44 
L 443.44181 224.64 
L 443.27058 224.64 
z
" style="fill:#d76b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.44181 224.64 
L 443.44181 496.44 
L 443.524574 496.44 
L 443.524574 224.64 
L 443.44181 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.524574 224.64 
L 443.524574 496.44 
L 443.782047 496.44 
L 443.782047 224.64 
L 443.524574 224.64 
z
" style="fill:#e7b1b1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 443.782047 224.64 
L 443.782047 496.44 
L 444.056207 496.44 
L 444.056207 224.64 
L 443.782047 224.64 
z
" style="fill:#d97575;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.060568 224.64 
L 444.060568 496.44 
L 444.12153 496.44 
L 444.12153 224.64 
L 444.060568 224.64 
z
" style="fill:#e09292;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.12153 224.64 
L 444.12153 496.44 
L 444.469188 496.44 
L 444.469188 224.64 
L 444.12153 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.469188 224.64 
L 444.469188 496.44 
L 444.540128 496.44 
L 444.540128 224.64 
L 444.469188 224.64 
z
" style="fill:#d45f5f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 444.540128 224.64 
L 444.540128 496.44 
L 445.263368 496.44 
L 445.263368 224.64 
L 444.540128 224.64 
z
" style="fill:#d97777;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.263368 224.64 
L 445.263368 496.44 
L 445.453548 496.44 
L 445.453548 224.64 
L 445.263368 224.64 
z
" style="fill:#dc8484;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.453548 224.64 
L 445.453548 496.44 
L 445.510904 496.44 
L 445.510904 224.64 
L 445.453548 224.64 
z
" style="fill:#d66a6a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.512833 224.64 
L 445.512833 496.44 
L 445.571111 496.44 
L 445.571111 224.64 
L 445.512833 224.64 
z
" style="fill:#d87171;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.573795 224.64 
L 445.573795 496.44 
L 445.7223 496.44 
L 445.7223 224.64 
L 445.573795 224.64 
z
" style="fill:#da7979;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.7223 224.64 
L 445.7223 496.44 
L 445.893697 496.44 
L 445.893697 224.64 
L 445.7223 224.64 
z
" style="fill:#d66b6b;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 445.893697 224.64 
L 445.893697 496.44 
L 446.610396 496.44 
L 446.610396 224.64 
L 445.893697 224.64 
z
" style="fill:#db7f7f;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.610396 224.64 
L 446.610396 496.44 
L 446.644189 496.44 
L 446.644189 224.64 
L 446.610396 224.64 
z
" style="fill:#e29a9a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 446.644189 224.64 
L 446.644189 496.44 
L 447.493042 496.44 
L 447.493042 224.64 
L 446.644189 224.64 
z
" style="fill:#da7a7a;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.493042 224.64 
L 447.493042 496.44 
L 447.83634 496.44 
L 447.83634 224.64 
L 447.493042 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 447.83634 224.64 
L 447.83634 496.44 
L 448.214437 496.44 
L 448.214437 224.64 
L 447.83634 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.214437 224.64 
L 448.214437 496.44 
L 448.34223 496.44 
L 448.34223 224.64 
L 448.214437 224.64 
z
" style="fill:#dc8181;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.34223 224.64 
L 448.34223 496.44 
L 448.545324 496.44 
L 448.545324 224.64 
L 448.34223 224.64 
z
" style="fill:#e09393;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.545743 224.64 
L 448.545743 496.44 
L 448.995284 496.44 
L 448.995284 224.64 
L 448.545743 224.64 
z
" style="fill:#da7c7c;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 448.995284 224.64 
L 448.995284 496.44 
L 449.65404 496.44 
L 449.65404 224.64 
L 448.995284 224.64 
z
" style="fill:#c41818;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 449.65404 224.64 
L 449.65404 496.44 
L 450.221647 496.44 
L 450.221647 224.64 
L 449.65404 224.64 
z
" style="fill:#c31414;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.221647 224.64 
L 450.221647 496.44 
L 450.933902 496.44 
L 450.933902 224.64 
L 450.221647 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 450.934321 224.64 
L 450.934321 496.44 
L 451.460252 496.44 
L 451.460252 224.64 
L 450.934321 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.461007 224.64 
L 451.461007 496.44 
L 451.490524 496.44 
L 451.490524 224.64 
L 451.461007 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.490943 224.64 
L 451.490943 496.44 
L 451.653619 496.44 
L 451.653619 224.64 
L 451.490943 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 451.654039 224.64 
L 451.654039 496.44 
L 452.179048 496.44 
L 452.179048 224.64 
L 451.654039 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.180222 224.64 
L 452.180222 496.44 
L 452.62666 496.44 
L 452.62666 224.64 
L 452.180222 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 452.627079 224.64 
L 452.627079 496.44 
L 453.256067 496.44 
L 453.256067 224.64 
L 452.627079 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.256067 224.64 
L 453.256067 496.44 
L 453.432411 496.44 
L 453.432411 224.64 
L 453.256067 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.437862 224.64 
L 453.437862 496.44 
L 453.655043 496.44 
L 453.655043 224.64 
L 453.437862 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.655043 224.64 
L 453.655043 496.44 
L 453.782585 496.44 
L 453.782585 224.64 
L 453.655043 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.782585 224.64 
L 453.782585 496.44 
L 453.989117 496.44 
L 453.989117 224.64 
L 453.782585 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 453.989537 224.64 
L 453.989537 496.44 
L 454.739442 496.44 
L 454.739442 224.64 
L 453.989537 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.739442 224.64 
L 454.739442 496.44 
L 454.779859 496.44 
L 454.779859 224.64 
L 454.739442 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 454.779859 224.64 
L 454.779859 496.44 
L 455.252208 496.44 
L 455.252208 224.64 
L 454.779859 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.252208 224.64 
L 455.252208 496.44 
L 455.343357 496.44 
L 455.343357 224.64 
L 455.252208 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.343357 224.64 
L 455.343357 496.44 
L 455.572194 496.44 
L 455.572194 224.64 
L 455.343357 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.572194 224.64 
L 455.572194 496.44 
L 455.885389 496.44 
L 455.885389 224.64 
L 455.572194 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 455.885389 224.64 
L 455.885389 496.44 
L 456.170995 496.44 
L 456.170995 224.64 
L 455.885389 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.170995 224.64 
L 456.170995 496.44 
L 456.764596 496.44 
L 456.764596 224.64 
L 456.170995 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.764596 224.64 
L 456.764596 496.44 
L 456.784554 496.44 
L 456.784554 224.64 
L 456.764596 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.784973 224.64 
L 456.784973 496.44 
L 456.951339 496.44 
L 456.951339 224.64 
L 456.784973 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 456.951339 224.64 
L 456.951339 496.44 
L 457.026724 496.44 
L 457.026724 224.64 
L 456.951339 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.026724 224.64 
L 457.026724 496.44 
L 457.188226 496.44 
L 457.188226 224.64 
L 457.026724 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.188226 224.64 
L 457.188226 496.44 
L 457.391572 496.44 
L 457.391572 224.64 
L 457.188226 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.391572 224.64 
L 457.391572 496.44 
L 457.463686 496.44 
L 457.463686 224.64 
L 457.391572 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.465866 224.64 
L 457.465866 496.44 
L 457.887316 496.44 
L 457.887316 224.64 
L 457.465866 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 457.887316 224.64 
L 457.887316 496.44 
L 458.196234 496.44 
L 458.196234 224.64 
L 457.887316 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.199923 224.64 
L 458.199923 496.44 
L 458.591772 496.44 
L 458.591772 224.64 
L 458.199923 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.591772 224.64 
L 458.591772 496.44 
L 458.705226 496.44 
L 458.705226 224.64 
L 458.591772 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.705226 224.64 
L 458.705226 496.44 
L 458.947564 496.44 
L 458.947564 224.64 
L 458.705226 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 458.947983 224.64 
L 458.947983 496.44 
L 459.312412 496.44 
L 459.312412 224.64 
L 458.947983 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.312412 224.64 
L 459.312412 496.44 
L 459.414882 496.44 
L 459.414882 224.64 
L 459.312412 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.415301 224.64 
L 459.415301 496.44 
L 459.785516 496.44 
L 459.785516 224.64 
L 459.415301 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.788199 224.64 
L 459.788199 496.44 
L 459.843962 496.44 
L 459.843962 224.64 
L 459.788199 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.847484 224.64 
L 459.847484 496.44 
L 459.95859 496.44 
L 459.95859 224.64 
L 459.847484 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 459.959177 224.64 
L 459.959177 496.44 
L 460.031879 496.44 
L 460.031879 224.64 
L 459.959177 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.031879 224.64 
L 460.031879 496.44 
L 460.074309 496.44 
L 460.074309 224.64 
L 460.031879 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.07825 224.64 
L 460.07825 496.44 
L 460.103909 496.44 
L 460.103909 224.64 
L 460.07825 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 460.104328 224.64 
L 460.104328 496.44 
L 460.129568 496.44 
L 460.129568 224.64 
L 460.104328 224.64 
z
" style="fill:#fdfafa;"/>
   </g>
   <g id="BrokenBarHCollection_105">
    <path clip-path="url(#p9901fb19d8)" d="M 463.319412 224.64 
L 463.319412 496.44 
L 463.373875 496.44 
L 463.373875 224.64 
L 463.319412 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.374294 224.64 
L 463.374294 496.44 
L 463.586277 496.44 
L 463.586277 224.64 
L 463.374294 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.586277 224.64 
L 463.586277 496.44 
L 463.918841 496.44 
L 463.918841 224.64 
L 463.586277 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 463.919428 224.64 
L 463.919428 496.44 
L 464.810627 496.44 
L 464.810627 224.64 
L 463.919428 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.810627 224.64 
L 464.810627 496.44 
L 464.867061 496.44 
L 464.867061 224.64 
L 464.810627 224.64 
z
" style="fill:#f9f2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 464.867061 224.64 
L 464.867061 496.44 
L 465.196942 496.44 
L 465.196942 224.64 
L 464.867061 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 465.197361 224.64 
L 465.197361 496.44 
L 466.008647 496.44 
L 466.008647 224.64 
L 465.197361 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.008647 224.64 
L 466.008647 496.44 
L 466.343476 496.44 
L 466.343476 224.64 
L 466.008647 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.343476 224.64 
L 466.343476 496.44 
L 466.71042 496.44 
L 466.71042 224.64 
L 466.343476 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.71042 224.64 
L 466.71042 496.44 
L 466.950242 496.44 
L 466.950242 224.64 
L 466.71042 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 466.950242 224.64 
L 466.950242 496.44 
L 467.168765 496.44 
L 467.168765 224.64 
L 466.950242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.169185 224.64 
L 467.169185 496.44 
L 467.301758 496.44 
L 467.301758 224.64 
L 467.169185 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.301758 224.64 
L 467.301758 496.44 
L 467.593066 496.44 
L 467.593066 224.64 
L 467.301758 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.593066 224.64 
L 467.593066 496.44 
L 467.699057 496.44 
L 467.699057 224.64 
L 467.593066 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.699057 224.64 
L 467.699057 496.44 
L 467.73327 496.44 
L 467.73327 224.64 
L 467.699057 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.73327 224.64 
L 467.73327 496.44 
L 467.860811 496.44 
L 467.860811 224.64 
L 467.73327 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 467.860811 224.64 
L 467.860811 496.44 
L 468.01636 496.44 
L 468.01636 224.64 
L 467.860811 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.01636 224.64 
L 468.01636 496.44 
L 468.311526 496.44 
L 468.311526 224.64 
L 468.01636 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.311526 224.64 
L 468.311526 496.44 
L 468.462295 496.44 
L 468.462295 224.64 
L 468.311526 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.462295 224.64 
L 468.462295 496.44 
L 468.630841 496.44 
L 468.630841 224.64 
L 468.462295 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.630841 224.64 
L 468.630841 496.44 
L 468.948312 496.44 
L 468.948312 224.64 
L 468.630841 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 468.948312 224.64 
L 468.948312 496.44 
L 469.211865 496.44 
L 469.211865 224.64 
L 468.948312 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 469.211865 224.64 
L 469.211865 496.44 
L 470.145662 496.44 
L 470.145662 224.64 
L 469.211865 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.145662 224.64 
L 470.145662 496.44 
L 470.440156 496.44 
L 470.440156 224.64 
L 470.145662 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 470.440156 224.64 
L 470.440156 496.44 
L 472.078242 496.44 
L 472.078242 224.64 
L 470.440156 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.078242 224.64 
L 472.078242 496.44 
L 472.461789 496.44 
L 472.461789 224.64 
L 472.078242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.461789 224.64 
L 472.461789 496.44 
L 472.662452 496.44 
L 472.662452 224.64 
L 472.461789 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 472.662452 224.64 
L 472.662452 496.44 
L 473.210017 496.44 
L 473.210017 224.64 
L 472.662452 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.210017 224.64 
L 473.210017 496.44 
L 473.431811 496.44 
L 473.431811 224.64 
L 473.210017 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.431811 224.64 
L 473.431811 496.44 
L 473.825337 496.44 
L 473.825337 224.64 
L 473.431811 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 473.825337 224.64 
L 473.825337 496.44 
L 475.958915 496.44 
L 475.958915 224.64 
L 473.825337 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 475.958915 224.64 
L 475.958915 496.44 
L 476.090062 496.44 
L 476.090062 224.64 
L 475.958915 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.090062 224.64 
L 476.090062 496.44 
L 476.251146 496.44 
L 476.251146 224.64 
L 476.090062 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.251146 224.64 
L 476.251146 496.44 
L 476.647355 496.44 
L 476.647355 224.64 
L 476.251146 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.647355 224.64 
L 476.647355 496.44 
L 476.720811 496.44 
L 476.720811 224.64 
L 476.647355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.720811 224.64 
L 476.720811 496.44 
L 476.885835 496.44 
L 476.885835 224.64 
L 476.720811 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.885835 224.64 
L 476.885835 496.44 
L 476.936064 496.44 
L 476.936064 224.64 
L 476.885835 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 476.936064 224.64 
L 476.936064 496.44 
L 477.311562 496.44 
L 477.311562 224.64 
L 476.936064 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 477.311562 224.64 
L 477.311562 496.44 
L 478.123351 496.44 
L 478.123351 224.64 
L 477.311562 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.123351 224.64 
L 478.123351 496.44 
L 478.522747 496.44 
L 478.522747 224.64 
L 478.123351 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.523166 224.64 
L 478.523166 496.44 
L 478.596035 496.44 
L 478.596035 224.64 
L 478.523166 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.596035 224.64 
L 478.596035 496.44 
L 478.86269 496.44 
L 478.86269 224.64 
L 478.596035 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.86269 224.64 
L 478.86269 496.44 
L 478.913422 496.44 
L 478.913422 224.64 
L 478.86269 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 478.913422 224.64 
L 478.913422 496.44 
L 479.069558 496.44 
L 479.069558 224.64 
L 478.913422 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.076266 224.64 
L 479.076266 496.44 
L 479.135467 496.44 
L 479.135467 224.64 
L 479.076266 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 479.135467 224.64 
L 479.135467 496.44 
L 479.43428 496.44 
L 479.43428 224.64 
L 479.135467 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_106">
    <path clip-path="url(#p9901fb19d8)" d="M 482.620769 224.64 
L 482.620769 496.44 
L 482.680515 496.44 
L 482.680515 224.64 
L 482.620769 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.680515 224.64 
L 482.680515 496.44 
L 482.935599 496.44 
L 482.935599 224.64 
L 482.680515 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 482.935599 224.64 
L 482.935599 496.44 
L 483.067333 496.44 
L 483.067333 224.64 
L 482.935599 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.067333 224.64 
L 483.067333 496.44 
L 483.176092 496.44 
L 483.176092 224.64 
L 483.067333 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.176092 224.64 
L 483.176092 496.44 
L 483.199655 496.44 
L 483.199655 224.64 
L 483.176092 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.199655 224.64 
L 483.199655 496.44 
L 483.225398 496.44 
L 483.225398 224.64 
L 483.199655 224.64 
z
" style="fill:#ebbfbf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.225398 224.64 
L 483.225398 496.44 
L 483.250135 496.44 
L 483.250135 224.64 
L 483.225398 224.64 
z
" style="fill:#e3a1a1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.250135 224.64 
L 483.250135 496.44 
L 483.284431 496.44 
L 483.284431 224.64 
L 483.250135 224.64 
z
" style="fill:#d87272;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.292481 224.64 
L 483.292481 496.44 
L 483.62689 496.44 
L 483.62689 224.64 
L 483.292481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.62689 224.64 
L 483.62689 496.44 
L 483.850864 496.44 
L 483.850864 224.64 
L 483.62689 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 483.851283 224.64 
L 483.851283 496.44 
L 484.688564 496.44 
L 484.688564 224.64 
L 483.851283 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 484.688564 224.64 
L 484.688564 496.44 
L 485.273529 496.44 
L 485.273529 224.64 
L 484.688564 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.273948 224.64 
L 485.273948 496.44 
L 485.850695 496.44 
L 485.850695 224.64 
L 485.273948 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 485.850695 224.64 
L 485.850695 496.44 
L 487.790235 496.44 
L 487.790235 224.64 
L 485.850695 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.790235 224.64 
L 487.790235 496.44 
L 487.891949 496.44 
L 487.891949 224.64 
L 487.790235 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 487.891949 224.64 
L 487.891949 496.44 
L 488.34694 496.44 
L 488.34694 224.64 
L 487.891949 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.34694 224.64 
L 488.34694 496.44 
L 488.577539 496.44 
L 488.577539 224.64 
L 488.34694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.577539 224.64 
L 488.577539 496.44 
L 488.708602 496.44 
L 488.708602 224.64 
L 488.577539 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.708602 224.64 
L 488.708602 496.44 
L 488.838911 496.44 
L 488.838911 224.64 
L 488.708602 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.838911 224.64 
L 488.838911 496.44 
L 488.962428 496.44 
L 488.962428 224.64 
L 488.838911 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 488.962428 224.64 
L 488.962428 496.44 
L 489.439724 496.44 
L 489.439724 224.64 
L 488.962428 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.439724 224.64 
L 489.439724 496.44 
L 489.647682 496.44 
L 489.647682 224.64 
L 489.439724 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.648101 224.64 
L 489.648101 496.44 
L 489.799289 496.44 
L 489.799289 224.64 
L 489.648101 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 489.799289 224.64 
L 489.799289 496.44 
L 490.000455 496.44 
L 490.000455 224.64 
L 489.799289 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.001042 224.64 
L 490.001042 496.44 
L 490.335954 496.44 
L 490.335954 224.64 
L 490.001042 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.335954 224.64 
L 490.335954 496.44 
L 490.432554 496.44 
L 490.432554 224.64 
L 490.335954 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.432554 224.64 
L 490.432554 496.44 
L 490.801679 496.44 
L 490.801679 224.64 
L 490.432554 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.801679 224.64 
L 490.801679 496.44 
L 490.940037 496.44 
L 490.940037 224.64 
L 490.801679 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 490.940037 224.64 
L 490.940037 496.44 
L 491.080828 496.44 
L 491.080828 224.64 
L 490.940037 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.080828 224.64 
L 491.080828 496.44 
L 491.271847 496.44 
L 491.271847 224.64 
L 491.080828 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.271847 224.64 
L 491.271847 496.44 
L 491.405091 496.44 
L 491.405091 224.64 
L 491.271847 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.405091 224.64 
L 491.405091 496.44 
L 491.54127 496.44 
L 491.54127 224.64 
L 491.405091 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.54127 224.64 
L 491.54127 496.44 
L 491.773126 496.44 
L 491.773126 224.64 
L 491.54127 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 491.773126 224.64 
L 491.773126 496.44 
L 492.002131 496.44 
L 492.002131 224.64 
L 491.773126 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.002131 224.64 
L 492.002131 496.44 
L 492.31893 496.44 
L 492.31893 224.64 
L 492.002131 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.31893 224.64 
L 492.31893 496.44 
L 492.437751 496.44 
L 492.437751 224.64 
L 492.31893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.437751 224.64 
L 492.437751 496.44 
L 492.513891 496.44 
L 492.513891 224.64 
L 492.437751 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.513891 224.64 
L 492.513891 496.44 
L 492.868676 496.44 
L 492.868676 224.64 
L 492.513891 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 492.868676 224.64 
L 492.868676 496.44 
L 493.087367 496.44 
L 493.087367 224.64 
L 492.868676 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.087367 224.64 
L 493.087367 496.44 
L 493.377669 496.44 
L 493.377669 224.64 
L 493.087367 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.378089 224.64 
L 493.378089 496.44 
L 493.769854 496.44 
L 493.769854 224.64 
L 493.378089 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 493.769854 224.64 
L 493.769854 496.44 
L 494.198263 496.44 
L 494.198263 224.64 
L 493.769854 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.198263 224.64 
L 494.198263 496.44 
L 494.326141 496.44 
L 494.326141 224.64 
L 494.198263 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.326141 224.64 
L 494.326141 496.44 
L 494.39641 496.44 
L 494.39641 224.64 
L 494.326141 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.39641 224.64 
L 494.39641 496.44 
L 494.527893 496.44 
L 494.527893 224.64 
L 494.39641 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.527893 224.64 
L 494.527893 496.44 
L 494.8405 496.44 
L 494.8405 224.64 
L 494.527893 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.8405 224.64 
L 494.8405 496.44 
L 494.968964 496.44 
L 494.968964 224.64 
L 494.8405 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 494.968964 224.64 
L 494.968964 496.44 
L 495.12661 496.44 
L 495.12661 224.64 
L 494.968964 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.12661 224.64 
L 495.12661 496.44 
L 495.279475 496.44 
L 495.279475 224.64 
L 495.12661 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.279475 224.64 
L 495.279475 496.44 
L 495.376662 496.44 
L 495.376662 224.64 
L 495.279475 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.376662 224.64 
L 495.376662 496.44 
L 495.427561 496.44 
L 495.427561 224.64 
L 495.376662 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.427561 224.64 
L 495.427561 496.44 
L 495.891944 496.44 
L 495.891944 224.64 
L 495.427561 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 495.891944 224.64 
L 495.891944 496.44 
L 496.14535 496.44 
L 496.14535 224.64 
L 495.891944 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 496.14535 224.64 
L 496.14535 496.44 
L 497.16124 496.44 
L 497.16124 224.64 
L 496.14535 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 497.161659 224.64 
L 497.161659 496.44 
L 497.427518 496.44 
L 497.427518 224.64 
L 497.161659 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_107">
    <path clip-path="url(#p9901fb19d8)" d="M 500.781715 224.64 
L 500.781715 496.44 
L 501.147359 496.44 
L 501.147359 224.64 
L 500.781715 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.147359 224.64 
L 501.147359 496.44 
L 501.166227 496.44 
L 501.166227 224.64 
L 501.147359 224.64 
z
" style="fill:#f7e9e9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.166646 224.64 
L 501.166646 496.44 
L 501.327226 496.44 
L 501.327226 224.64 
L 501.166646 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.327226 224.64 
L 501.327226 496.44 
L 501.349112 496.44 
L 501.349112 224.64 
L 501.327226 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 501.349112 224.64 
L 501.349112 496.44 
L 502.048034 496.44 
L 502.048034 224.64 
L 501.349112 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.048453 224.64 
L 502.048453 496.44 
L 502.224127 496.44 
L 502.224127 224.64 
L 502.048453 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.224546 224.64 
L 502.224546 496.44 
L 502.238466 496.44 
L 502.238466 224.64 
L 502.224546 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.23964 224.64 
L 502.23964 496.44 
L 502.28425 496.44 
L 502.28425 224.64 
L 502.23964 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.28425 224.64 
L 502.28425 496.44 
L 502.522898 496.44 
L 502.522898 224.64 
L 502.28425 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.522898 224.64 
L 502.522898 496.44 
L 502.577068 496.44 
L 502.577068 224.64 
L 502.522898 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.577906 224.64 
L 502.577906 496.44 
L 502.596522 496.44 
L 502.596522 224.64 
L 502.577906 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.597025 224.64 
L 502.597025 496.44 
L 502.746285 496.44 
L 502.746285 224.64 
L 502.597025 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.746285 224.64 
L 502.746285 496.44 
L 502.999188 496.44 
L 502.999188 224.64 
L 502.746285 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 502.999188 224.64 
L 502.999188 496.44 
L 503.236746 496.44 
L 503.236746 224.64 
L 502.999188 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.236746 224.64 
L 503.236746 496.44 
L 503.268108 496.44 
L 503.268108 224.64 
L 503.236746 224.64 
z
" style="fill:#dd8989;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.270372 224.64 
L 503.270372 496.44 
L 503.836637 496.44 
L 503.836637 224.64 
L 503.270372 224.64 
z
" style="fill:#dd8787;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.836637 224.64 
L 503.836637 496.44 
L 503.948582 496.44 
L 503.948582 224.64 
L 503.836637 224.64 
z
" style="fill:#e19999;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 503.948582 224.64 
L 503.948582 496.44 
L 504.082413 496.44 
L 504.082413 224.64 
L 503.948582 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.082413 224.64 
L 504.082413 496.44 
L 504.276786 496.44 
L 504.276786 224.64 
L 504.082413 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.276786 224.64 
L 504.276786 496.44 
L 504.480886 496.44 
L 504.480886 224.64 
L 504.276786 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.480886 224.64 
L 504.480886 496.44 
L 504.603481 496.44 
L 504.603481 224.64 
L 504.480886 224.64 
z
" style="fill:#8080db;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 504.603481 224.64 
L 504.603481 496.44 
L 505.410322 496.44 
L 505.410322 224.64 
L 504.603481 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.410322 224.64 
L 505.410322 496.44 
L 505.600587 496.44 
L 505.600587 224.64 
L 505.410322 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.600587 224.64 
L 505.600587 496.44 
L 505.911685 496.44 
L 505.911685 224.64 
L 505.600587 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 505.911685 224.64 
L 505.911685 496.44 
L 506.01885 496.44 
L 506.01885 224.64 
L 505.911685 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.01885 224.64 
L 506.01885 496.44 
L 506.375313 496.44 
L 506.375313 224.64 
L 506.01885 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.375313 224.64 
L 506.375313 496.44 
L 506.688004 496.44 
L 506.688004 224.64 
L 506.375313 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.689094 224.64 
L 506.689094 496.44 
L 506.761544 496.44 
L 506.761544 224.64 
L 506.689094 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 506.761544 224.64 
L 506.761544 496.44 
L 507.158592 496.44 
L 507.158592 224.64 
L 506.761544 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.158592 224.64 
L 507.158592 496.44 
L 507.240265 496.44 
L 507.240265 224.64 
L 507.158592 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.240265 224.64 
L 507.240265 496.44 
L 507.327977 496.44 
L 507.327977 224.64 
L 507.240265 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.327977 224.64 
L 507.327977 496.44 
L 507.576687 496.44 
L 507.576687 224.64 
L 507.327977 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.576687 224.64 
L 507.576687 496.44 
L 507.994112 496.44 
L 507.994112 224.64 
L 507.576687 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 507.994112 224.64 
L 507.994112 496.44 
L 508.248105 496.44 
L 508.248105 224.64 
L 507.994112 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.248105 224.64 
L 508.248105 496.44 
L 508.528093 496.44 
L 508.528093 224.64 
L 508.248105 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.528093 224.64 
L 508.528093 496.44 
L 508.583856 496.44 
L 508.583856 224.64 
L 508.528093 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.583856 224.64 
L 508.583856 496.44 
L 508.833489 496.44 
L 508.833489 224.64 
L 508.583856 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 508.833489 224.64 
L 508.833489 496.44 
L 509.136117 496.44 
L 509.136117 224.64 
L 508.833489 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.136117 224.64 
L 509.136117 496.44 
L 509.261898 496.44 
L 509.261898 224.64 
L 509.136117 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.261898 224.64 
L 509.261898 496.44 
L 509.318583 496.44 
L 509.318583 224.64 
L 509.261898 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.318583 224.64 
L 509.318583 496.44 
L 509.572325 496.44 
L 509.572325 224.64 
L 509.318583 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 509.572325 224.64 
L 509.572325 496.44 
L 510.006521 496.44 
L 510.006521 224.64 
L 509.572325 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 510.00694 224.64 
L 510.00694 496.44 
L 511.159176 496.44 
L 511.159176 224.64 
L 510.00694 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.159176 224.64 
L 511.159176 496.44 
L 511.280596 496.44 
L 511.280596 224.64 
L 511.159176 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.280596 224.64 
L 511.280596 496.44 
L 511.289066 496.44 
L 511.289066 224.64 
L 511.280596 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.296529 224.64 
L 511.296529 496.44 
L 511.311287 496.44 
L 511.311287 224.64 
L 511.296529 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.311706 224.64 
L 511.311706 496.44 
L 511.328645 496.44 
L 511.328645 224.64 
L 511.311706 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.329064 224.64 
L 511.329064 496.44 
L 511.340887 496.44 
L 511.340887 224.64 
L 511.329064 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.340887 224.64 
L 511.340887 496.44 
L 511.34944 496.44 
L 511.34944 224.64 
L 511.340887 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.357993 224.64 
L 511.357993 496.44 
L 511.36814 496.44 
L 511.36814 224.64 
L 511.357993 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.371158 224.64 
L 511.371158 496.44 
L 511.380131 496.44 
L 511.380131 224.64 
L 511.371158 224.64 
z
" style="fill:#efcfcf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.380131 224.64 
L 511.380131 496.44 
L 511.511614 496.44 
L 511.511614 224.64 
L 511.380131 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.511614 224.64 
L 511.511614 496.44 
L 511.665653 496.44 
L 511.665653 224.64 
L 511.511614 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 511.665653 224.64 
L 511.665653 496.44 
L 512.457234 496.44 
L 512.457234 224.64 
L 511.665653 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.457234 224.64 
L 512.457234 496.44 
L 512.529683 496.44 
L 512.529683 224.64 
L 512.457234 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 512.530103 224.64 
L 512.530103 496.44 
L 513.126891 496.44 
L 513.126891 224.64 
L 512.530103 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.126891 224.64 
L 513.126891 496.44 
L 513.28353 496.44 
L 513.28353 224.64 
L 513.126891 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.283949 224.64 
L 513.283949 496.44 
L 513.371828 496.44 
L 513.371828 224.64 
L 513.283949 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 513.371828 224.64 
L 513.371828 496.44 
L 514.06379 496.44 
L 514.06379 224.64 
L 513.371828 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.06379 224.64 
L 514.06379 496.44 
L 514.621041 496.44 
L 514.621041 224.64 
L 514.06379 224.64 
z
" style="fill:#fbf7f7;"/>
   </g>
   <g id="BrokenBarHCollection_108">
    <path clip-path="url(#p9901fb19d8)" d="M 514.634793 224.64 
L 514.634793 496.44 
L 514.714119 496.44 
L 514.714119 224.64 
L 514.634793 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 514.714119 224.64 
L 514.714119 496.44 
L 515.463856 496.44 
L 515.463856 224.64 
L 514.714119 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 515.463856 224.64 
L 515.463856 496.44 
L 516.015363 496.44 
L 516.015363 224.64 
L 515.463856 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.015363 224.64 
L 516.015363 496.44 
L 516.22374 496.44 
L 516.22374 224.64 
L 516.015363 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.22374 224.64 
L 516.22374 496.44 
L 516.441509 496.44 
L 516.441509 224.64 
L 516.22374 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.441509 224.64 
L 516.441509 496.44 
L 516.75529 496.44 
L 516.75529 224.64 
L 516.441509 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 516.75529 224.64 
L 516.75529 496.44 
L 517.100768 496.44 
L 517.100768 224.64 
L 516.75529 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.101187 224.64 
L 517.101187 496.44 
L 517.112256 496.44 
L 517.112256 224.64 
L 517.101187 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.112675 224.64 
L 517.112675 496.44 
L 517.258245 496.44 
L 517.258245 224.64 
L 517.112675 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.258245 224.64 
L 517.258245 496.44 
L 517.360966 496.44 
L 517.360966 224.64 
L 517.258245 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.360966 224.64 
L 517.360966 496.44 
L 517.384781 496.44 
L 517.384781 224.64 
L 517.360966 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.386793 224.64 
L 517.386793 496.44 
L 517.40566 496.44 
L 517.40566 224.64 
L 517.386793 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.411614 224.64 
L 517.411614 496.44 
L 517.432578 496.44 
L 517.432578 224.64 
L 517.411614 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.432997 224.64 
L 517.432997 496.44 
L 517.72288 496.44 
L 517.72288 224.64 
L 517.432997 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.730678 224.64 
L 517.730678 496.44 
L 517.901237 496.44 
L 517.901237 224.64 
L 517.730678 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 517.901237 224.64 
L 517.901237 496.44 
L 518.072047 496.44 
L 518.072047 224.64 
L 517.901237 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.072466 224.64 
L 518.072466 496.44 
L 518.390105 496.44 
L 518.390105 224.64 
L 518.072466 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.390105 224.64 
L 518.390105 496.44 
L 518.404025 496.44 
L 518.404025 224.64 
L 518.390105 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.404025 224.64 
L 518.404025 496.44 
L 518.61215 496.44 
L 518.61215 224.64 
L 518.404025 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.61215 224.64 
L 518.61215 496.44 
L 518.699609 496.44 
L 518.699609 224.64 
L 518.61215 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.699609 224.64 
L 518.699609 496.44 
L 518.771472 496.44 
L 518.771472 224.64 
L 518.699609 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.771472 224.64 
L 518.771472 496.44 
L 518.842664 496.44 
L 518.842664 224.64 
L 518.771472 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 518.842664 224.64 
L 518.842664 496.44 
L 519.149569 496.44 
L 519.149569 224.64 
L 518.842664 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.149569 224.64 
L 519.149569 496.44 
L 519.384025 496.44 
L 519.384025 224.64 
L 519.149569 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.384444 224.64 
L 519.384444 496.44 
L 519.431989 496.44 
L 519.431989 224.64 
L 519.384444 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.445573 224.64 
L 519.445573 496.44 
L 519.502594 496.44 
L 519.502594 224.64 
L 519.445573 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.502594 224.64 
L 519.502594 496.44 
L 519.561711 496.44 
L 519.561711 224.64 
L 519.502594 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.562382 224.64 
L 519.562382 496.44 
L 519.691936 496.44 
L 519.691936 224.64 
L 519.562382 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 519.692355 224.64 
L 519.692355 496.44 
L 520.036156 496.44 
L 520.036156 224.64 
L 519.692355 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.036156 224.64 
L 520.036156 496.44 
L 520.098124 496.44 
L 520.098124 224.64 
L 520.036156 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.098124 224.64 
L 520.098124 496.44 
L 520.124454 496.44 
L 520.124454 224.64 
L 520.098124 224.64 
z
" style="fill:#f3dede;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.124454 224.64 
L 520.124454 496.44 
L 520.175941 496.44 
L 520.175941 224.64 
L 520.124454 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.175941 224.64 
L 520.175941 496.44 
L 520.204703 496.44 
L 520.204703 224.64 
L 520.175941 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.204703 224.64 
L 520.204703 496.44 
L 520.233884 496.44 
L 520.233884 224.64 
L 520.204703 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.233884 224.64 
L 520.233884 496.44 
L 520.296355 496.44 
L 520.296355 224.64 
L 520.233884 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.296355 224.64 
L 520.296355 496.44 
L 520.359665 496.44 
L 520.359665 224.64 
L 520.296355 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.359665 224.64 
L 520.359665 496.44 
L 520.520915 496.44 
L 520.520915 224.64 
L 520.359665 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 520.520915 224.64 
L 520.520915 496.44 
L 521.469512 496.44 
L 521.469512 224.64 
L 520.520915 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 521.469512 224.64 
L 521.469512 496.44 
L 522.404273 496.44 
L 522.404273 224.64 
L 521.469512 224.64 
z
" style="fill:#c7c7ed;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.404273 224.64 
L 522.404273 496.44 
L 522.413833 496.44 
L 522.413833 224.64 
L 522.404273 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.413833 224.64 
L 522.413833 496.44 
L 522.738599 496.44 
L 522.738599 224.64 
L 522.413833 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 522.738599 224.64 
L 522.738599 496.44 
L 523.061604 496.44 
L 523.061604 224.64 
L 522.738599 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.061604 224.64 
L 523.061604 496.44 
L 523.149567 496.44 
L 523.149567 224.64 
L 523.061604 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.149567 224.64 
L 523.149567 496.44 
L 523.411023 496.44 
L 523.411023 224.64 
L 523.149567 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.411023 224.64 
L 523.411023 496.44 
L 523.696629 496.44 
L 523.696629 224.64 
L 523.411023 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.696629 224.64 
L 523.696629 496.44 
L 523.846895 496.44 
L 523.846895 224.64 
L 523.696629 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.846895 224.64 
L 523.846895 496.44 
L 523.983326 496.44 
L 523.983326 224.64 
L 523.846895 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 523.983745 224.64 
L 523.983745 496.44 
L 524.11875 496.44 
L 524.11875 224.64 
L 523.983745 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.11875 224.64 
L 524.11875 496.44 
L 524.36637 496.44 
L 524.36637 224.64 
L 524.11875 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 524.36637 224.64 
L 524.36637 496.44 
L 525.504015 496.44 
L 525.504015 224.64 
L 524.36637 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.504015 224.64 
L 525.504015 496.44 
L 525.710967 496.44 
L 525.710967 224.64 
L 525.504015 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 525.710967 224.64 
L 525.710967 496.44 
L 526.115394 496.44 
L 526.115394 224.64 
L 525.710967 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.115394 224.64 
L 526.115394 496.44 
L 526.216857 496.44 
L 526.216857 224.64 
L 526.115394 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.216857 224.64 
L 526.216857 496.44 
L 526.787315 496.44 
L 526.787315 224.64 
L 526.216857 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 526.787315 224.64 
L 526.787315 496.44 
L 527.055396 496.44 
L 527.055396 224.64 
L 526.787315 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.055815 224.64 
L 527.055815 496.44 
L 527.641954 496.44 
L 527.641954 224.64 
L 527.055815 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.641954 224.64 
L 527.641954 496.44 
L 527.867185 496.44 
L 527.867185 224.64 
L 527.641954 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 527.867185 224.64 
L 527.867185 496.44 
L 528.114386 496.44 
L 528.114386 224.64 
L 527.867185 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.114386 224.64 
L 528.114386 496.44 
L 528.259202 496.44 
L 528.259202 224.64 
L 528.114386 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.259202 224.64 
L 528.259202 496.44 
L 528.33291 496.44 
L 528.33291 224.64 
L 528.259202 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.33291 224.64 
L 528.33291 496.44 
L 528.47957 496.44 
L 528.47957 224.64 
L 528.33291 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.47957 224.64 
L 528.47957 496.44 
L 528.661365 496.44 
L 528.661365 224.64 
L 528.47957 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.661365 224.64 
L 528.661365 496.44 
L 528.996026 496.44 
L 528.996026 224.64 
L 528.661365 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 528.996026 224.64 
L 528.996026 496.44 
L 529.376135 496.44 
L 529.376135 224.64 
L 528.996026 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.376135 224.64 
L 529.376135 496.44 
L 529.630129 496.44 
L 529.630129 224.64 
L 529.376135 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 529.630129 224.64 
L 529.630129 496.44 
L 529.764085 496.44 
L 529.764085 224.64 
L 529.630129 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_109">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764128 224.64 
L 529.764128 496.44 
L 530.237273 496.44 
L 530.237273 224.64 
L 529.764128 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.237273 224.64 
L 530.237273 496.44 
L 530.707106 496.44 
L 530.707106 224.64 
L 530.237273 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.707106 224.64 
L 530.707106 496.44 
L 530.851335 496.44 
L 530.851335 224.64 
L 530.707106 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 530.851335 224.64 
L 530.851335 496.44 
L 531.254588 496.44 
L 531.254588 224.64 
L 530.851335 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.254588 224.64 
L 531.254588 496.44 
L 531.303894 496.44 
L 531.303894 224.64 
L 531.254588 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.303894 224.64 
L 531.303894 496.44 
L 531.390683 496.44 
L 531.390683 224.64 
L 531.303894 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.390683 224.64 
L 531.390683 496.44 
L 531.517638 496.44 
L 531.517638 224.64 
L 531.390683 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.517638 224.64 
L 531.517638 496.44 
L 531.712514 496.44 
L 531.712514 224.64 
L 531.517638 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.712514 224.64 
L 531.712514 496.44 
L 531.834605 496.44 
L 531.834605 224.64 
L 531.712514 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 531.835025 224.64 
L 531.835025 496.44 
L 532.006422 496.44 
L 532.006422 224.64 
L 531.835025 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.006841 224.64 
L 532.006841 496.44 
L 532.570507 496.44 
L 532.570507 224.64 
L 532.006841 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.570507 224.64 
L 532.570507 496.44 
L 532.959673 496.44 
L 532.959673 224.64 
L 532.570507 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 532.972754 224.64 
L 532.972754 496.44 
L 533.001013 496.44 
L 533.001013 224.64 
L 532.972754 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.001013 224.64 
L 533.001013 496.44 
L 533.267333 496.44 
L 533.267333 224.64 
L 533.001013 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.267333 224.64 
L 533.267333 496.44 
L 533.358566 496.44 
L 533.358566 224.64 
L 533.267333 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.358566 224.64 
L 533.358566 496.44 
L 533.494744 496.44 
L 533.494744 224.64 
L 533.358566 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.494744 224.64 
L 533.494744 496.44 
L 533.749367 496.44 
L 533.749367 224.64 
L 533.494744 224.64 
z
" style="fill:#d1d1f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 533.749367 224.64 
L 533.749367 496.44 
L 534.623585 496.44 
L 534.623585 224.64 
L 533.749367 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.623585 224.64 
L 534.623585 496.44 
L 534.701905 496.44 
L 534.701905 224.64 
L 534.623585 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.701905 224.64 
L 534.701905 496.44 
L 534.811334 496.44 
L 534.811334 224.64 
L 534.701905 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.811334 224.64 
L 534.811334 496.44 
L 534.945416 496.44 
L 534.945416 224.64 
L 534.811334 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 534.945416 224.64 
L 534.945416 496.44 
L 535.165029 496.44 
L 535.165029 224.64 
L 534.945416 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.165029 224.64 
L 535.165029 496.44 
L 535.227081 496.44 
L 535.227081 224.64 
L 535.165029 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.227081 224.64 
L 535.227081 496.44 
L 535.730624 496.44 
L 535.730624 224.64 
L 535.227081 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.730624 224.64 
L 535.730624 496.44 
L 535.845671 496.44 
L 535.845671 224.64 
L 535.730624 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 535.846174 224.64 
L 535.846174 496.44 
L 537.206284 496.44 
L 537.206284 224.64 
L 535.846174 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.210645 224.64 
L 537.210645 496.44 
L 537.225151 496.44 
L 537.225151 224.64 
L 537.210645 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.225571 224.64 
L 537.225571 496.44 
L 537.237394 496.44 
L 537.237394 224.64 
L 537.225571 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.242174 224.64 
L 537.242174 496.44 
L 537.261376 496.44 
L 537.261376 224.64 
L 537.242174 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.26473 224.64 
L 537.26473 496.44 
L 537.600733 496.44 
L 537.600733 224.64 
L 537.26473 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.600733 224.64 
L 537.600733 496.44 
L 537.66203 496.44 
L 537.66203 224.64 
L 537.600733 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 537.66203 224.64 
L 537.66203 496.44 
L 538.005579 496.44 
L 538.005579 224.64 
L 537.66203 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.005579 224.64 
L 538.005579 496.44 
L 538.24515 496.44 
L 538.24515 224.64 
L 538.005579 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 538.24515 224.64 
L 538.24515 496.44 
L 539.058616 496.44 
L 539.058616 224.64 
L 538.24515 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.058616 224.64 
L 539.058616 496.44 
L 539.264226 496.44 
L 539.264226 224.64 
L 539.058616 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.264226 224.64 
L 539.264226 496.44 
L 539.303721 496.44 
L 539.303721 224.64 
L 539.264226 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.303721 224.64 
L 539.303721 496.44 
L 539.499771 496.44 
L 539.499771 224.64 
L 539.303721 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.499771 224.64 
L 539.499771 496.44 
L 539.524844 496.44 
L 539.524844 224.64 
L 539.499771 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.525263 224.64 
L 539.525263 496.44 
L 539.565597 496.44 
L 539.565597 224.64 
L 539.525263 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.565597 224.64 
L 539.565597 496.44 
L 539.752842 496.44 
L 539.752842 224.64 
L 539.565597 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 539.752842 224.64 
L 539.752842 496.44 
L 540.012454 496.44 
L 540.012454 224.64 
L 539.752842 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.012454 224.64 
L 540.012454 496.44 
L 540.331182 496.44 
L 540.331182 224.64 
L 540.012454 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.331182 224.64 
L 540.331182 496.44 
L 540.50149 496.44 
L 540.50149 224.64 
L 540.331182 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.50149 224.64 
L 540.50149 496.44 
L 540.718252 496.44 
L 540.718252 224.64 
L 540.50149 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.718252 224.64 
L 540.718252 496.44 
L 540.844955 496.44 
L 540.844955 224.64 
L 540.718252 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 540.844955 224.64 
L 540.844955 496.44 
L 541.053248 496.44 
L 541.053248 224.64 
L 540.844955 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.053248 224.64 
L 541.053248 496.44 
L 541.111191 496.44 
L 541.111191 224.64 
L 541.053248 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.111191 224.64 
L 541.111191 496.44 
L 541.245022 496.44 
L 541.245022 224.64 
L 541.111191 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.245441 224.64 
L 541.245441 496.44 
L 541.437215 496.44 
L 541.437215 224.64 
L 541.245441 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.437634 224.64 
L 541.437634 496.44 
L 541.73607 496.44 
L 541.73607 224.64 
L 541.437634 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.73607 224.64 
L 541.73607 496.44 
L 541.91862 496.44 
L 541.91862 224.64 
L 541.73607 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 541.91862 224.64 
L 541.91862 496.44 
L 542.763615 496.44 
L 542.763615 224.64 
L 541.91862 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 542.764035 224.64 
L 542.764035 496.44 
L 543.197811 496.44 
L 543.197811 224.64 
L 542.764035 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.197811 224.64 
L 543.197811 496.44 
L 543.368202 496.44 
L 543.368202 224.64 
L 543.197811 224.64 
z
" style="fill:#e6e6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.368202 224.64 
L 543.368202 496.44 
L 543.381133 496.44 
L 543.381133 224.64 
L 543.368202 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_110">
    <path clip-path="url(#p9901fb19d8)" d="M 543.390022 224.64 
L 543.390022 496.44 
L 543.398994 496.44 
L 543.398994 224.64 
L 543.390022 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.399917 224.64 
L 543.399917 496.44 
L 543.545403 496.44 
L 543.545403 224.64 
L 543.399917 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.545403 224.64 
L 543.545403 496.44 
L 543.811304 496.44 
L 543.811304 224.64 
L 543.545403 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.811304 224.64 
L 543.811304 496.44 
L 543.948321 496.44 
L 543.948321 224.64 
L 543.811304 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 543.948321 224.64 
L 543.948321 496.44 
L 544.170198 496.44 
L 544.170198 224.64 
L 543.948321 224.64 
z
" style="fill:#6d6dd7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.170617 224.64 
L 544.170617 496.44 
L 544.274009 496.44 
L 544.274009 224.64 
L 544.170617 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.274429 224.64 
L 544.274429 496.44 
L 544.414716 496.44 
L 544.414716 224.64 
L 544.274429 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.414716 224.64 
L 544.414716 496.44 
L 544.561628 496.44 
L 544.561628 224.64 
L 544.414716 224.64 
z
" style="fill:#5757d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.561628 224.64 
L 544.561628 496.44 
L 544.651855 496.44 
L 544.651855 224.64 
L 544.561628 224.64 
z
" style="fill:#4343ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.651855 224.64 
L 544.651855 496.44 
L 544.847821 496.44 
L 544.847821 224.64 
L 544.651855 224.64 
z
" style="fill:#5b5bd3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.847821 224.64 
L 544.847821 496.44 
L 544.914988 496.44 
L 544.914988 224.64 
L 544.847821 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 544.914988 224.64 
L 544.914988 496.44 
L 545.1907 496.44 
L 545.1907 224.64 
L 544.914988 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.1907 224.64 
L 545.1907 496.44 
L 545.388511 496.44 
L 545.388511 224.64 
L 545.1907 224.64 
z
" style="fill:#6767d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.388511 224.64 
L 545.388511 496.44 
L 545.417524 496.44 
L 545.417524 224.64 
L 545.388511 224.64 
z
" style="fill:#7e7edb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.418698 224.64 
L 545.418698 496.44 
L 545.427755 496.44 
L 545.427755 224.64 
L 545.418698 224.64 
z
" style="fill:#6464d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.428342 224.64 
L 545.428342 496.44 
L 545.957879 496.44 
L 545.957879 224.64 
L 545.428342 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 545.957879 224.64 
L 545.957879 496.44 
L 546.225582 496.44 
L 546.225582 224.64 
L 545.957879 224.64 
z
" style="fill:#4848cf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.225582 224.64 
L 546.225582 496.44 
L 546.857211 496.44 
L 546.857211 224.64 
L 546.225582 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 546.857211 224.64 
L 546.857211 496.44 
L 547.03146 496.44 
L 547.03146 224.64 
L 546.857211 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.03146 224.64 
L 547.03146 496.44 
L 547.316311 496.44 
L 547.316311 224.64 
L 547.03146 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.316311 224.64 
L 547.316311 496.44 
L 547.471106 496.44 
L 547.471106 224.64 
L 547.316311 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.471106 224.64 
L 547.471106 496.44 
L 547.589088 496.44 
L 547.589088 224.64 
L 547.471106 224.64 
z
" style="fill:#6565d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.589759 224.64 
L 547.589759 496.44 
L 547.787319 496.44 
L 547.787319 224.64 
L 547.589759 224.64 
z
" style="fill:#7373d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 547.788241 224.64 
L 547.788241 496.44 
L 548.16508 496.44 
L 548.16508 224.64 
L 547.788241 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.16508 224.64 
L 548.16508 496.44 
L 548.844213 496.44 
L 548.844213 224.64 
L 548.16508 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.844213 224.64 
L 548.844213 496.44 
L 548.964543 496.44 
L 548.964543 224.64 
L 548.844213 224.64 
z
" style="fill:#8989dd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 548.964543 224.64 
L 548.964543 496.44 
L 549.148518 496.44 
L 549.148518 224.64 
L 548.964543 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.148518 224.64 
L 549.148518 496.44 
L 549.325366 496.44 
L 549.325366 224.64 
L 549.148518 224.64 
z
" style="fill:#6262d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.325366 224.64 
L 549.325366 496.44 
L 549.731638 496.44 
L 549.731638 224.64 
L 549.325366 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.731638 224.64 
L 549.731638 496.44 
L 549.899094 496.44 
L 549.899094 224.64 
L 549.731638 224.64 
z
" style="fill:#7f7fdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 549.899598 224.64 
L 549.899598 496.44 
L 550.520787 496.44 
L 550.520787 224.64 
L 549.899598 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.520787 224.64 
L 550.520787 496.44 
L 550.80698 496.44 
L 550.80698 224.64 
L 550.520787 224.64 
z
" style="fill:#6969d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.80698 224.64 
L 550.80698 496.44 
L 550.851339 496.44 
L 550.851339 224.64 
L 550.80698 224.64 
z
" style="fill:#4d4dd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.852597 224.64 
L 550.852597 496.44 
L 550.923034 496.44 
L 550.923034 224.64 
L 550.852597 224.64 
z
" style="fill:#5e5ed4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 550.923034 224.64 
L 550.923034 496.44 
L 551.319327 496.44 
L 551.319327 224.64 
L 550.923034 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.319327 224.64 
L 551.319327 496.44 
L 551.479237 496.44 
L 551.479237 224.64 
L 551.319327 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 551.479237 224.64 
L 551.479237 496.44 
L 552.053216 496.44 
L 552.053216 224.64 
L 551.479237 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.053216 224.64 
L 552.053216 496.44 
L 552.425444 496.44 
L 552.425444 224.64 
L 552.053216 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.425863 224.64 
L 552.425863 496.44 
L 552.596086 496.44 
L 552.596086 224.64 
L 552.425863 224.64 
z
" style="fill:#7474d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.596506 224.64 
L 552.596506 496.44 
L 552.659648 496.44 
L 552.659648 224.64 
L 552.596506 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.659648 224.64 
L 552.659648 496.44 
L 552.937204 496.44 
L 552.937204 224.64 
L 552.659648 224.64 
z
" style="fill:#5e5ed3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 552.937204 224.64 
L 552.937204 496.44 
L 553.36838 496.44 
L 553.36838 224.64 
L 552.937204 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 553.36838 224.64 
L 553.36838 496.44 
L 554.075269 496.44 
L 554.075269 224.64 
L 553.36838 224.64 
z
" style="fill:#7d7ddb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.075688 224.64 
L 554.075688 496.44 
L 554.699644 496.44 
L 554.699644 224.64 
L 554.075688 224.64 
z
" style="fill:#7b7bda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.699644 224.64 
L 554.699644 496.44 
L 554.887309 496.44 
L 554.887309 224.64 
L 554.699644 224.64 
z
" style="fill:#6060d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 554.887309 224.64 
L 554.887309 496.44 
L 555.227337 496.44 
L 555.227337 224.64 
L 554.887309 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.22784 224.64 
L 555.22784 496.44 
L 555.799891 496.44 
L 555.799891 224.64 
L 555.22784 224.64 
z
" style="fill:#7575d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.799891 224.64 
L 555.799891 496.44 
L 555.956195 496.44 
L 555.956195 224.64 
L 555.799891 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 555.956195 224.64 
L 555.956195 496.44 
L 556.274085 496.44 
L 556.274085 224.64 
L 555.956195 224.64 
z
" style="fill:#6161d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.274085 224.64 
L 556.274085 496.44 
L 556.465146 496.44 
L 556.465146 224.64 
L 556.274085 224.64 
z
" style="fill:#7676d9;"/>
   </g>
   <g id="BrokenBarHCollection_111">
    <path clip-path="url(#p9901fb19d8)" d="M 556.487367 224.64 
L 556.487367 496.44 
L 556.499526 496.44 
L 556.499526 224.64 
L 556.487367 224.64 
z
" style="fill:#f8eded;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.500532 224.64 
L 556.500532 496.44 
L 556.613987 496.44 
L 556.613987 224.64 
L 556.500532 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 556.613987 224.64 
L 556.613987 496.44 
L 557.690251 496.44 
L 557.690251 224.64 
L 556.613987 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.693605 224.64 
L 557.693605 496.44 
L 557.818044 496.44 
L 557.818044 224.64 
L 557.693605 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 557.818044 224.64 
L 557.818044 496.44 
L 558.017113 496.44 
L 558.017113 224.64 
L 557.818044 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.017113 224.64 
L 558.017113 496.44 
L 558.686183 496.44 
L 558.686183 224.64 
L 558.017113 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.686183 224.64 
L 558.686183 496.44 
L 558.834856 496.44 
L 558.834856 224.64 
L 558.686183 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 558.835276 224.64 
L 558.835276 496.44 
L 559.040382 496.44 
L 559.040382 224.64 
L 558.835276 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.040382 224.64 
L 559.040382 496.44 
L 559.278863 496.44 
L 559.278863 224.64 
L 559.040382 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 559.278863 224.64 
L 559.278863 496.44 
L 560.125284 496.44 
L 560.125284 224.64 
L 559.278863 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.125703 224.64 
L 560.125703 496.44 
L 560.566774 496.44 
L 560.566774 224.64 
L 560.125703 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.566774 224.64 
L 560.566774 496.44 
L 560.592098 496.44 
L 560.592098 224.64 
L 560.566774 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.592517 224.64 
L 560.592517 496.44 
L 560.856028 496.44 
L 560.856028 224.64 
L 560.592517 224.64 
z
" style="fill:#fcfcfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 560.856028 224.64 
L 560.856028 496.44 
L 561.178656 496.44 
L 561.178656 224.64 
L 560.856028 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.178656 224.64 
L 561.178656 496.44 
L 561.900554 496.44 
L 561.900554 224.64 
L 561.178656 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 561.900554 224.64 
L 561.900554 496.44 
L 562.111782 496.44 
L 562.111782 224.64 
L 561.900554 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.111782 224.64 
L 562.111782 496.44 
L 562.185405 496.44 
L 562.185405 224.64 
L 562.111782 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.185405 224.64 
L 562.185405 496.44 
L 562.343218 496.44 
L 562.343218 224.64 
L 562.185405 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.343218 224.64 
L 562.343218 496.44 
L 562.631089 496.44 
L 562.631089 224.64 
L 562.343218 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.635617 224.64 
L 562.635617 496.44 
L 562.799048 496.44 
L 562.799048 224.64 
L 562.635617 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.802738 224.64 
L 562.802738 496.44 
L 562.967091 496.44 
L 562.967091 224.64 
L 562.802738 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 562.967091 224.64 
L 562.967091 496.44 
L 563.494867 496.44 
L 563.494867 224.64 
L 562.967091 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.494867 224.64 
L 563.494867 496.44 
L 563.624589 496.44 
L 563.624589 224.64 
L 563.494867 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.624589 224.64 
L 563.624589 496.44 
L 563.821059 496.44 
L 563.821059 224.64 
L 563.624589 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.821478 224.64 
L 563.821478 496.44 
L 563.904158 496.44 
L 563.904158 224.64 
L 563.821478 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 563.904158 224.64 
L 563.904158 496.44 
L 564.015851 496.44 
L 564.015851 224.64 
L 563.904158 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.015851 224.64 
L 564.015851 496.44 
L 564.953589 496.44 
L 564.953589 224.64 
L 564.015851 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 564.954344 224.64 
L 564.954344 496.44 
L 565.113918 496.44 
L 565.113918 224.64 
L 564.954344 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.113918 224.64 
L 565.113918 496.44 
L 565.526311 496.44 
L 565.526311 224.64 
L 565.113918 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.526311 224.64 
L 565.526311 496.44 
L 565.638004 496.44 
L 565.638004 224.64 
L 565.526311 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.638004 224.64 
L 565.638004 496.44 
L 565.740306 496.44 
L 565.740306 224.64 
L 565.638004 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 565.749195 224.64 
L 565.749195 496.44 
L 566.119913 496.44 
L 566.119913 224.64 
L 565.749195 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.119913 224.64 
L 566.119913 496.44 
L 566.13769 496.44 
L 566.13769 224.64 
L 566.119913 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.13769 224.64 
L 566.13769 496.44 
L 566.291226 496.44 
L 566.291226 224.64 
L 566.13769 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.291226 224.64 
L 566.291226 496.44 
L 566.379734 496.44 
L 566.379734 224.64 
L 566.291226 224.64 
z
" style="fill:#fdfbfb;"/>
   </g>
   <g id="BrokenBarHCollection_112">
    <path clip-path="url(#p9901fb19d8)" d="M 566.389839 224.64 
L 566.389839 496.44 
L 566.515745 496.44 
L 566.515745 224.64 
L 566.389839 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.515745 224.64 
L 566.515745 496.44 
L 566.773596 496.44 
L 566.773596 224.64 
L 566.515745 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 566.773596 224.64 
L 566.773596 496.44 
L 567.097104 496.44 
L 567.097104 224.64 
L 566.773596 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.097104 224.64 
L 567.097104 496.44 
L 567.314034 496.44 
L 567.314034 224.64 
L 567.097104 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.314034 224.64 
L 567.314034 496.44 
L 567.711334 496.44 
L 567.711334 224.64 
L 567.314034 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.711334 224.64 
L 567.711334 496.44 
L 567.839714 496.44 
L 567.839714 224.64 
L 567.711334 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 567.839714 224.64 
L 567.839714 496.44 
L 568.045743 496.44 
L 568.045743 224.64 
L 567.839714 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.045743 224.64 
L 568.045743 496.44 
L 568.257893 496.44 
L 568.257893 224.64 
L 568.045743 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 568.257893 224.64 
L 568.257893 496.44 
L 569.280072 496.44 
L 569.280072 224.64 
L 568.257893 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.280072 224.64 
L 569.280072 496.44 
L 569.965242 496.44 
L 569.965242 224.64 
L 569.280072 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 569.965242 224.64 
L 569.965242 496.44 
L 570.079786 496.44 
L 570.079786 224.64 
L 569.965242 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.080289 224.64 
L 570.080289 496.44 
L 570.235419 496.44 
L 570.235419 224.64 
L 570.080289 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.235419 224.64 
L 570.235419 496.44 
L 570.30812 496.44 
L 570.30812 224.64 
L 570.235419 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.30812 224.64 
L 570.30812 496.44 
L 570.534861 496.44 
L 570.534861 224.64 
L 570.30812 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.534861 224.64 
L 570.534861 496.44 
L 570.622321 496.44 
L 570.622321 224.64 
L 570.534861 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.622321 224.64 
L 570.622321 496.44 
L 570.700053 496.44 
L 570.700053 224.64 
L 570.622321 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.708103 224.64 
L 570.708103 496.44 
L 570.73871 496.44 
L 570.73871 224.64 
L 570.708103 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.739129 224.64 
L 570.739129 496.44 
L 570.748856 496.44 
L 570.748856 224.64 
L 570.739129 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.748856 224.64 
L 570.748856 496.44 
L 570.783991 496.44 
L 570.783991 224.64 
L 570.748856 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 570.783991 224.64 
L 570.783991 496.44 
L 571.053707 496.44 
L 571.053707 224.64 
L 570.783991 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.053707 224.64 
L 571.053707 496.44 
L 571.467232 496.44 
L 571.467232 224.64 
L 571.053707 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.467232 224.64 
L 571.467232 496.44 
L 571.547313 496.44 
L 571.547313 224.64 
L 571.467232 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.547313 224.64 
L 571.547313 496.44 
L 571.771622 496.44 
L 571.771622 224.64 
L 571.547313 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 571.771622 224.64 
L 571.771622 496.44 
L 572.339648 496.44 
L 572.339648 224.64 
L 571.771622 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.339648 224.64 
L 572.339648 496.44 
L 572.3856 496.44 
L 572.3856 224.64 
L 572.339648 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.3856 224.64 
L 572.3856 496.44 
L 572.643702 496.44 
L 572.643702 224.64 
L 572.3856 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.643702 224.64 
L 572.643702 496.44 
L 572.918491 496.44 
L 572.918491 224.64 
L 572.643702 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 572.918491 224.64 
L 572.918491 496.44 
L 573.065319 496.44 
L 573.065319 224.64 
L 572.918491 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.065319 224.64 
L 573.065319 496.44 
L 573.47461 496.44 
L 573.47461 224.64 
L 573.065319 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.47461 224.64 
L 573.47461 496.44 
L 573.973289 496.44 
L 573.973289 224.64 
L 573.47461 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 573.973289 224.64 
L 573.973289 496.44 
L 574.137139 496.44 
L 574.137139 224.64 
L 573.973289 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.137139 224.64 
L 574.137139 496.44 
L 574.567058 496.44 
L 574.567058 224.64 
L 574.137139 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.567058 224.64 
L 574.567058 496.44 
L 574.603115 496.44 
L 574.603115 224.64 
L 574.567058 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.603115 224.64 
L 574.603115 496.44 
L 574.753885 496.44 
L 574.753885 224.64 
L 574.603115 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.753885 224.64 
L 574.753885 496.44 
L 574.809899 496.44 
L 574.809899 224.64 
L 574.753885 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.809899 224.64 
L 574.809899 496.44 
L 574.914632 496.44 
L 574.914632 224.64 
L 574.809899 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 574.914632 224.64 
L 574.914632 496.44 
L 575.056681 496.44 
L 575.056681 224.64 
L 574.914632 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.056681 224.64 
L 575.056681 496.44 
L 575.720887 496.44 
L 575.720887 224.64 
L 575.056681 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 575.720887 224.64 
L 575.720887 496.44 
L 576.081878 496.44 
L 576.081878 224.64 
L 575.720887 224.64 
z
" style="fill:#f8ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.081878 224.64 
L 576.081878 496.44 
L 576.263338 496.44 
L 576.263338 224.64 
L 576.081878 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.263338 224.64 
L 576.263338 496.44 
L 576.529742 496.44 
L 576.529742 224.64 
L 576.263338 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.529742 224.64 
L 576.529742 496.44 
L 576.788179 496.44 
L 576.788179 224.64 
L 576.529742 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 576.788179 224.64 
L 576.788179 496.44 
L 576.939494 496.44 
L 576.939494 224.64 
L 576.788179 224.64 
z
" style="fill:#fbf5f5;"/>
   </g>
   <g id="BrokenBarHCollection_113">
    <path clip-path="url(#p9901fb19d8)" d="M 578.538587 224.64 
L 578.538587 496.44 
L 578.562234 496.44 
L 578.562234 224.64 
L 578.538587 224.64 
z
" style="fill:#e0e0f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.573387 224.64 
L 578.573387 496.44 
L 578.600304 496.44 
L 578.600304 224.64 
L 578.573387 224.64 
z
" style="fill:#ebebf7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.614727 224.64 
L 578.614727 496.44 
L 578.63351 496.44 
L 578.63351 224.64 
L 578.614727 224.64 
z
" style="fill:#e7e7f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.63351 224.64 
L 578.63351 496.44 
L 578.67812 496.44 
L 578.67812 224.64 
L 578.63351 224.64 
z
" style="fill:#fdfdfe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.67812 224.64 
L 578.67812 496.44 
L 578.729397 496.44 
L 578.729397 224.64 
L 578.67812 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.729397 224.64 
L 578.729397 496.44 
L 578.760884 496.44 
L 578.760884 224.64 
L 578.729397 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.760884 224.64 
L 578.760884 496.44 
L 578.786292 496.44 
L 578.786292 224.64 
L 578.760884 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 578.786292 224.64 
L 578.786292 496.44 
L 579.07999 496.44 
L 579.07999 224.64 
L 578.786292 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.07999 224.64 
L 579.07999 496.44 
L 579.349706 496.44 
L 579.349706 224.64 
L 579.07999 224.64 
z
" style="fill:#fefeff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.349706 224.64 
L 579.349706 496.44 
L 579.457374 496.44 
L 579.457374 224.64 
L 579.349706 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.457374 224.64 
L 579.457374 496.44 
L 579.481776 496.44 
L 579.481776 224.64 
L 579.457374 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 579.48471 224.64 
L 579.48471 496.44 
L 580.015757 496.44 
L 580.015757 224.64 
L 579.48471 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.016176 224.64 
L 580.016176 496.44 
L 580.147072 496.44 
L 580.147072 224.64 
L 580.016176 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 580.147072 224.64 
L 580.147072 496.44 
L 581.080533 496.44 
L 581.080533 224.64 
L 580.147072 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.080533 224.64 
L 581.080533 496.44 
L 581.473389 496.44 
L 581.473389 224.64 
L 581.080533 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.473389 224.64 
L 581.473389 496.44 
L 581.670194 496.44 
L 581.670194 224.64 
L 581.473389 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 581.670194 224.64 
L 581.670194 496.44 
L 582.339599 496.44 
L 582.339599 224.64 
L 581.670194 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.339599 224.64 
L 582.339599 496.44 
L 582.51041 496.44 
L 582.51041 224.64 
L 582.339599 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.51041 224.64 
L 582.51041 496.44 
L 582.659669 496.44 
L 582.659669 224.64 
L 582.51041 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.659669 224.64 
L 582.659669 496.44 
L 582.757778 496.44 
L 582.757778 224.64 
L 582.659669 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.757778 224.64 
L 582.757778 496.44 
L 582.871904 496.44 
L 582.871904 224.64 
L 582.757778 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 582.871904 224.64 
L 582.871904 496.44 
L 583.081287 496.44 
L 583.081287 224.64 
L 582.871904 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.081287 224.64 
L 583.081287 496.44 
L 583.222916 496.44 
L 583.222916 224.64 
L 583.081287 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.222916 224.64 
L 583.222916 496.44 
L 583.294946 496.44 
L 583.294946 224.64 
L 583.222916 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.294946 224.64 
L 583.294946 496.44 
L 583.441858 496.44 
L 583.441858 224.64 
L 583.294946 224.64 
z
" style="fill:#fcfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.441858 224.64 
L 583.441858 496.44 
L 583.750273 496.44 
L 583.750273 224.64 
L 583.441858 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 583.750273 224.64 
L 583.750273 496.44 
L 584.077638 496.44 
L 584.077638 224.64 
L 583.750273 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.077638 224.64 
L 584.077638 496.44 
L 584.21323 496.44 
L 584.21323 224.64 
L 584.077638 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.21323 224.64 
L 584.21323 496.44 
L 584.88448 496.44 
L 584.88448 224.64 
L 584.21323 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 584.88448 224.64 
L 584.88448 496.44 
L 585.009464 496.44 
L 585.009464 224.64 
L 584.88448 224.64 
z
" style="fill:#fcf9f9;"/>
   </g>
   <g id="BrokenBarHCollection_114">
    <path clip-path="url(#p9901fb19d8)" d="M 587.711236 224.64 
L 587.711236 496.44 
L 587.740418 496.44 
L 587.740418 224.64 
L 587.711236 224.64 
z
" style="fill:#dcdcf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.745617 224.64 
L 587.745617 496.44 
L 587.769431 496.44 
L 587.769431 224.64 
L 587.745617 224.64 
z
" style="fill:#d6d6f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.769431 224.64 
L 587.769431 496.44 
L 587.803979 496.44 
L 587.803979 224.64 
L 587.769431 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.808423 224.64 
L 587.808423 496.44 
L 587.822385 496.44 
L 587.822385 224.64 
L 587.808423 224.64 
z
" style="fill:#f4e0e0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.822385 224.64 
L 587.822385 496.44 
L 587.854459 496.44 
L 587.854459 224.64 
L 587.822385 224.64 
z
" style="fill:#6666d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.860832 224.64 
L 587.860832 496.44 
L 587.88691 496.44 
L 587.88691 224.64 
L 587.860832 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.907035 224.64 
L 587.907035 496.44 
L 587.989715 496.44 
L 587.989715 224.64 
L 587.907035 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 587.991141 224.64 
L 587.991141 496.44 
L 588.141323 496.44 
L 588.141323 224.64 
L 587.991141 224.64 
z
" style="fill:#7171d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.172768 224.64 
L 588.172768 496.44 
L 588.417705 496.44 
L 588.417705 224.64 
L 588.172768 224.64 
z
" style="fill:#8282dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.448899 224.64 
L 588.448899 496.44 
L 588.466341 496.44 
L 588.466341 224.64 
L 588.448899 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.467514 224.64 
L 588.467514 496.44 
L 588.476403 496.44 
L 588.476403 224.64 
L 588.467514 224.64 
z
" style="fill:#3f3fcd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.481602 224.64 
L 588.481602 496.44 
L 588.615013 496.44 
L 588.615013 224.64 
L 588.481602 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.632287 224.64 
L 588.632287 496.44 
L 588.643775 496.44 
L 588.643775 224.64 
L 588.632287 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.663649 224.64 
L 588.663649 496.44 
L 588.67413 496.44 
L 588.67413 224.64 
L 588.663649 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.683103 224.64 
L 588.683103 496.44 
L 588.832195 496.44 
L 588.832195 224.64 
L 588.683103 224.64 
z
" style="fill:#7272d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.832195 224.64 
L 588.832195 496.44 
L 588.860873 496.44 
L 588.860873 224.64 
L 588.832195 224.64 
z
" style="fill:#4f4fd0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 588.860873 224.64 
L 588.860873 496.44 
L 589.067237 496.44 
L 589.067237 224.64 
L 588.860873 224.64 
z
" style="fill:#7676d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.06774 224.64 
L 589.06774 496.44 
L 589.080402 496.44 
L 589.080402 224.64 
L 589.06774 224.64 
z
" style="fill:#8f8fdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.091974 224.64 
L 589.091974 496.44 
L 589.101282 496.44 
L 589.101282 224.64 
L 589.091974 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.101282 224.64 
L 589.101282 496.44 
L 589.214736 496.44 
L 589.214736 224.64 
L 589.101282 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.214736 224.64 
L 589.214736 496.44 
L 589.271254 496.44 
L 589.271254 224.64 
L 589.214736 224.64 
z
" style="fill:#5959d3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.277207 224.64 
L 589.277207 496.44 
L 589.74159 496.44 
L 589.74159 224.64 
L 589.277207 224.64 
z
" style="fill:#6868d6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 589.748047 224.64 
L 589.748047 496.44 
L 590.040194 496.44 
L 590.040194 224.64 
L 589.748047 224.64 
z
" style="fill:#7070d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.045141 224.64 
L 590.045141 496.44 
L 590.338546 496.44 
L 590.338546 224.64 
L 590.045141 224.64 
z
" style="fill:#7c7cda;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.339384 224.64 
L 590.339384 496.44 
L 590.478162 496.44 
L 590.478162 224.64 
L 590.339384 224.64 
z
" style="fill:#6a6ad6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.478162 224.64 
L 590.478162 496.44 
L 590.552541 496.44 
L 590.552541 224.64 
L 590.478162 224.64 
z
" style="fill:#5151d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.558578 224.64 
L 590.558578 496.44 
L 590.822802 496.44 
L 590.822802 224.64 
L 590.558578 224.64 
z
" style="fill:#4646ce;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.822802 224.64 
L 590.822802 496.44 
L 590.920827 496.44 
L 590.920827 224.64 
L 590.822802 224.64 
z
" style="fill:#5858d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 590.920827 224.64 
L 590.920827 496.44 
L 591.056922 496.44 
L 591.056922 224.64 
L 590.920827 224.64 
z
" style="fill:#6e6ed7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.056922 224.64 
L 591.056922 496.44 
L 591.117884 496.44 
L 591.117884 224.64 
L 591.056922 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.117884 224.64 
L 591.117884 496.44 
L 591.132474 496.44 
L 591.132474 224.64 
L 591.117884 224.64 
z
" style="fill:#5454d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.132474 224.64 
L 591.132474 496.44 
L 591.238717 496.44 
L 591.238717 224.64 
L 591.132474 224.64 
z
" style="fill:#7a7ada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.239472 224.64 
L 591.239472 496.44 
L 591.367517 496.44 
L 591.367517 224.64 
L 591.239472 224.64 
z
" style="fill:#8b8bde;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.367517 224.64 
L 591.367517 496.44 
L 591.599373 496.44 
L 591.599373 224.64 
L 591.367517 224.64 
z
" style="fill:#7979da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.600127 224.64 
L 591.600127 496.44 
L 591.856636 496.44 
L 591.856636 224.64 
L 591.600127 224.64 
z
" style="fill:#8383dc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 591.856636 224.64 
L 591.856636 496.44 
L 592.343324 496.44 
L 592.343324 224.64 
L 591.856636 224.64 
z
" style="fill:#7777d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.343324 224.64 
L 592.343324 496.44 
L 592.612327 496.44 
L 592.612327 224.64 
L 592.343324 224.64 
z
" style="fill:#6363d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.612327 224.64 
L 592.612327 496.44 
L 592.971222 496.44 
L 592.971222 224.64 
L 592.612327 224.64 
z
" style="fill:#7878da;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 592.971222 224.64 
L 592.971222 496.44 
L 593.070253 496.44 
L 593.070253 224.64 
L 592.971222 224.64 
z
" style="fill:#5555d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.070253 224.64 
L 593.070253 496.44 
L 593.323408 496.44 
L 593.323408 224.64 
L 593.070253 224.64 
z
" style="fill:#4040cd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.323408 224.64 
L 593.323408 496.44 
L 593.385208 496.44 
L 593.385208 224.64 
L 593.323408 224.64 
z
" style="fill:#5252d1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.385208 224.64 
L 593.385208 496.44 
L 593.603522 496.44 
L 593.603522 224.64 
L 593.385208 224.64 
z
" style="fill:#6f6fd7;"/>
   </g>
   <g id="BrokenBarHCollection_115">
    <path clip-path="url(#p9901fb19d8)" d="M 593.613627 224.64 
L 593.613627 496.44 
L 593.69224 496.44 
L 593.69224 224.64 
L 593.613627 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.692659 224.64 
L 593.692659 496.44 
L 593.853323 496.44 
L 593.853323 224.64 
L 593.692659 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 593.853826 224.64 
L 593.853826 496.44 
L 594.174483 496.44 
L 594.174483 224.64 
L 593.853826 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.174903 224.64 
L 594.174903 496.44 
L 594.229995 496.44 
L 594.229995 224.64 
L 594.174903 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.229995 224.64 
L 594.229995 496.44 
L 594.244585 496.44 
L 594.244585 224.64 
L 594.229995 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 594.245172 224.64 
L 594.245172 496.44 
L 595.108364 496.44 
L 595.108364 224.64 
L 594.245172 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.108364 224.64 
L 595.108364 496.44 
L 595.781123 496.44 
L 595.781123 224.64 
L 595.108364 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 595.781123 224.64 
L 595.781123 496.44 
L 596.322149 496.44 
L 596.322149 224.64 
L 595.781123 224.64 
z
" style="fill:#f7ebeb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.322149 224.64 
L 596.322149 496.44 
L 596.429481 496.44 
L 596.429481 224.64 
L 596.322149 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 596.429481 224.64 
L 596.429481 496.44 
L 597.52998 496.44 
L 597.52998 224.64 
L 596.429481 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 597.52998 224.64 
L 597.52998 496.44 
L 599.212759 496.44 
L 599.212759 224.64 
L 597.52998 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.212759 224.64 
L 599.212759 496.44 
L 599.243701 496.44 
L 599.243701 224.64 
L 599.212759 224.64 
z
" style="fill:#0000bf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 599.243701 224.64 
L 599.243701 496.44 
L 600.050711 496.44 
L 600.050711 224.64 
L 599.243701 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.050711 224.64 
L 600.050711 496.44 
L 600.180684 496.44 
L 600.180684 224.64 
L 600.050711 224.64 
z
" style="fill:#f6e7e7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 600.180684 224.64 
L 600.180684 496.44 
L 601.911428 496.44 
L 601.911428 224.64 
L 600.180684 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 601.911428 224.64 
L 601.911428 496.44 
L 602.228731 496.44 
L 602.228731 224.64 
L 601.911428 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.22915 224.64 
L 602.22915 496.44 
L 602.288016 496.44 
L 602.288016 224.64 
L 602.22915 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.288016 224.64 
L 602.288016 496.44 
L 602.341347 496.44 
L 602.341347 224.64 
L 602.288016 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.341347 224.64 
L 602.341347 496.44 
L 602.418996 496.44 
L 602.418996 224.64 
L 602.341347 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.418996 224.64 
L 602.418996 496.44 
L 602.441888 496.44 
L 602.441888 224.64 
L 602.418996 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.441888 224.64 
L 602.441888 496.44 
L 602.457065 496.44 
L 602.457065 224.64 
L 602.441888 224.64 
z
" style="fill:#f5e3e3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.457484 224.64 
L 602.457484 496.44 
L 602.625276 496.44 
L 602.625276 224.64 
L 602.457484 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 602.625276 224.64 
L 602.625276 496.44 
L 603.388933 496.44 
L 603.388933 224.64 
L 602.625276 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.388933 224.64 
L 603.388933 496.44 
L 603.688166 496.44 
L 603.688166 224.64 
L 603.388933 224.64 
z
" style="fill:#fffefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.688166 224.64 
L 603.688166 496.44 
L 603.955115 496.44 
L 603.955115 224.64 
L 603.688166 224.64 
z
" style="fill:#ddddf3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.955115 224.64 
L 603.955115 496.44 
L 603.977587 496.44 
L 603.977587 224.64 
L 603.955115 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 603.977587 224.64 
L 603.977587 496.44 
L 604.061357 496.44 
L 604.061357 224.64 
L 603.977587 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.061357 224.64 
L 604.061357 496.44 
L 604.078715 496.44 
L 604.078715 224.64 
L 604.061357 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.079134 224.64 
L 604.079134 496.44 
L 604.838096 496.44 
L 604.838096 224.64 
L 604.079134 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 604.838096 224.64 
L 604.838096 496.44 
L 605.394969 496.44 
L 605.394969 224.64 
L 604.838096 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.394969 224.64 
L 605.394969 496.44 
L 605.503895 496.44 
L 605.503895 224.64 
L 605.394969 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.510855 224.64 
L 605.510855 496.44 
L 605.586408 496.44 
L 605.586408 224.64 
L 605.510855 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.586408 224.64 
L 605.586408 496.44 
L 605.672861 496.44 
L 605.672861 224.64 
L 605.586408 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 605.67328 224.64 
L 605.67328 496.44 
L 606.551314 496.44 
L 606.551314 224.64 
L 605.67328 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 606.551314 224.64 
L 606.551314 496.44 
L 609.434042 496.44 
L 609.434042 224.64 
L 606.551314 224.64 
z
" style="fill:#f9f1f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.434462 224.64 
L 609.434462 496.44 
L 609.609129 496.44 
L 609.609129 224.64 
L 609.434462 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.609129 224.64 
L 609.609129 496.44 
L 609.887692 496.44 
L 609.887692 224.64 
L 609.609129 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 609.887692 224.64 
L 609.887692 496.44 
L 610.306961 496.44 
L 610.306961 224.64 
L 609.887692 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.306961 224.64 
L 610.306961 496.44 
L 610.381843 496.44 
L 610.381843 224.64 
L 610.306961 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.381843 224.64 
L 610.381843 496.44 
L 610.619233 496.44 
L 610.619233 224.64 
L 610.381843 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.628121 224.64 
L 610.628121 496.44 
L 610.637932 496.44 
L 610.637932 224.64 
L 610.628121 224.64 
z
" style="fill:#f7e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.644305 224.64 
L 610.644305 496.44 
L 610.659986 496.44 
L 610.659986 224.64 
L 610.644305 224.64 
z
" style="fill:#f1d5d5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 610.659986 224.64 
L 610.659986 496.44 
L 611.718725 496.44 
L 611.718725 224.64 
L 610.659986 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 611.719228 224.64 
L 611.719228 496.44 
L 612.005589 496.44 
L 612.005589 224.64 
L 611.719228 224.64 
z
" style="fill:#f9f0f0;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.005589 224.64 
L 612.005589 496.44 
L 612.216481 496.44 
L 612.216481 224.64 
L 612.005589 224.64 
z
" style="fill:#fefcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.216481 224.64 
L 612.216481 496.44 
L 612.788952 496.44 
L 612.788952 224.64 
L 612.216481 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.788952 224.64 
L 612.788952 496.44 
L 612.909534 496.44 
L 612.909534 224.64 
L 612.788952 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 612.909534 224.64 
L 612.909534 496.44 
L 614.467455 496.44 
L 614.467455 224.64 
L 612.909534 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 614.468796 224.64 
L 614.468796 496.44 
L 615.01066 496.44 
L 615.01066 224.64 
L 614.468796 224.64 
z
" style="fill:#f9efef;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.01066 224.64 
L 615.01066 496.44 
L 615.702119 496.44 
L 615.702119 224.64 
L 615.01066 224.64 
z
" style="fill:#fbf6f6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.702119 224.64 
L 615.702119 496.44 
L 615.955022 496.44 
L 615.955022 224.64 
L 615.702119 224.64 
z
" style="fill:#fefefe;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 615.955022 224.64 
L 615.955022 496.44 
L 616.010953 496.44 
L 616.010953 224.64 
L 615.955022 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.010953 224.64 
L 616.010953 496.44 
L 616.232327 496.44 
L 616.232327 224.64 
L 616.010953 224.64 
z
" style="fill:#f7eaea;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.232746 224.64 
L 616.232746 496.44 
L 616.399112 496.44 
L 616.399112 224.64 
L 616.232746 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 616.399112 224.64 
L 616.399112 496.44 
L 617.138703 496.44 
L 617.138703 224.64 
L 616.399112 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.139123 224.64 
L 617.139123 496.44 
L 617.229601 496.44 
L 617.229601 224.64 
L 617.139123 224.64 
z
" style="fill:#fbf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.23002 224.64 
L 617.23002 496.44 
L 617.674991 496.44 
L 617.674991 224.64 
L 617.23002 224.64 
z
" style="fill:#faf2f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 617.679645 224.64 
L 617.679645 496.44 
L 618.53596 496.44 
L 618.53596 224.64 
L 617.679645 224.64 
z
" style="fill:#faf3f3;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.53596 224.64 
L 618.53596 496.44 
L 618.756496 496.44 
L 618.756496 224.64 
L 618.53596 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.756496 224.64 
L 618.756496 496.44 
L 618.94131 496.44 
L 618.94131 224.64 
L 618.756496 224.64 
z
" style="fill:#fcf9f9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 618.941729 224.64 
L 618.941729 496.44 
L 619.072793 496.44 
L 619.072793 224.64 
L 618.941729 224.64 
z
" style="fill:#fcf7f7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.072793 224.64 
L 619.072793 496.44 
L 619.083442 496.44 
L 619.083442 224.64 
L 619.072793 224.64 
z
" style="fill:#f2d9d9;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.083862 224.64 
L 619.083862 496.44 
L 619.408376 496.44 
L 619.408376 224.64 
L 619.083862 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.409298 224.64 
L 619.409298 496.44 
L 619.53097 496.44 
L 619.53097 224.64 
L 619.409298 224.64 
z
" style="fill:#f8eeee;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.531809 224.64 
L 619.531809 496.44 
L 619.547574 496.44 
L 619.547574 224.64 
L 619.531809 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 619.547993 224.64 
L 619.547993 496.44 
L 619.641867 496.44 
L 619.641867 224.64 
L 619.547993 224.64 
z
" style="fill:#fcf8f8;"/>
   </g>
   <g id="BrokenBarHCollection_116">
    <path clip-path="url(#p9901fb19d8)" d="M 620.086335 224.64 
L 620.086335 496.44 
L 620.687274 496.44 
L 620.687274 224.64 
L 620.086335 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 620.703961 224.64 
L 620.703961 496.44 
L 621.187714 496.44 
L 621.187714 224.64 
L 620.703961 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.188217 224.64 
L 621.188217 496.44 
L 621.240038 496.44 
L 621.240038 224.64 
L 621.188217 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.240038 224.64 
L 621.240038 496.44 
L 621.269639 496.44 
L 621.269639 224.64 
L 621.240038 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.269639 224.64 
L 621.269639 496.44 
L 621.32951 496.44 
L 621.32951 224.64 
L 621.269639 224.64 
z
" style="fill:#fdfbfb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.336051 224.64 
L 621.336051 496.44 
L 621.588074 496.44 
L 621.588074 224.64 
L 621.336051 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.588074 224.64 
L 621.588074 496.44 
L 621.842025 496.44 
L 621.842025 224.64 
L 621.588074 224.64 
z
" style="fill:#fafafd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.842445 224.64 
L 621.842445 496.44 
L 621.937451 496.44 
L 621.937451 224.64 
L 621.842445 224.64 
z
" style="fill:#ffffff;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.937451 224.64 
L 621.937451 496.44 
L 621.946004 496.44 
L 621.946004 224.64 
L 621.937451 224.64 
z
" style="fill:#d5d5f1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.946004 224.64 
L 621.946004 496.44 
L 621.971915 496.44 
L 621.971915 224.64 
L 621.946004 224.64 
z
" style="fill:#fbfbfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 621.971915 224.64 
L 621.971915 496.44 
L 622.004283 496.44 
L 622.004283 224.64 
L 621.971915 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.004702 224.64 
L 622.004702 496.44 
L 622.110693 496.44 
L 622.110693 224.64 
L 622.004702 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.110693 224.64 
L 622.110693 496.44 
L 622.387411 496.44 
L 622.387411 224.64 
L 622.110693 224.64 
z
" style="fill:#faf4f4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.387411 224.64 
L 622.387411 496.44 
L 622.706643 496.44 
L 622.706643 224.64 
L 622.387411 224.64 
z
" style="fill:#fdfafa;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.707649 224.64 
L 622.707649 496.44 
L 622.745215 496.44 
L 622.745215 224.64 
L 622.707649 224.64 
z
" style="fill:#f6e8e8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.745215 224.64 
L 622.745215 496.44 
L 622.892882 496.44 
L 622.892882 224.64 
L 622.745215 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.893301 224.64 
L 622.893301 496.44 
L 622.923405 496.44 
L 622.923405 224.64 
L 622.893301 224.64 
z
" style="fill:#fdfcfc;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 622.923405 224.64 
L 622.923405 496.44 
L 623.16851 496.44 
L 623.16851 224.64 
L 622.923405 224.64 
z
" style="fill:#f2dada;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.16851 224.64 
L 623.16851 496.44 
L 623.414285 496.44 
L 623.414285 224.64 
L 623.16851 224.64 
z
" style="fill:#fcf8f8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.414705 224.64 
L 623.414705 496.44 
L 623.669033 496.44 
L 623.669033 224.64 
L 623.414705 224.64 
z
" style="fill:#f8ecec;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.67809 224.64 
L 623.67809 496.44 
L 623.707438 496.44 
L 623.707438 224.64 
L 623.67809 224.64 
z
" style="fill:#f6e6e6;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.707858 224.64 
L 623.707858 496.44 
L 623.726222 496.44 
L 623.726222 224.64 
L 623.707858 224.64 
z
" style="fill:#f0d2d2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.726222 224.64 
L 623.726222 496.44 
L 623.754984 496.44 
L 623.754984 224.64 
L 623.726222 224.64 
z
" style="fill:#fbf5f5;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.754984 224.64 
L 623.754984 496.44 
L 623.883028 496.44 
L 623.883028 224.64 
L 623.754984 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.883448 224.64 
L 623.883448 496.44 
L 623.902986 496.44 
L 623.902986 224.64 
L 623.883448 224.64 
z
" style="fill:#f1d4d4;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 623.9107 224.64 
L 623.9107 496.44 
L 624.076982 496.44 
L 624.076982 224.64 
L 623.9107 224.64 
z
" style="fill:#f1d7d7;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.077402 224.64 
L 624.077402 496.44 
L 624.094005 496.44 
L 624.094005 224.64 
L 624.077402 224.64 
z
" style="fill:#f2d8d8;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.094424 224.64 
L 624.094424 496.44 
L 624.118826 496.44 
L 624.118826 224.64 
L 624.094424 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.119245 224.64 
L 624.119245 496.44 
L 624.138112 496.44 
L 624.138112 224.64 
L 624.119245 224.64 
z
" style="fill:#f3dddd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.138531 224.64 
L 624.138531 496.44 
L 624.236892 496.44 
L 624.236892 224.64 
L 624.138531 224.64 
z
" style="fill:#f2dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.237311 224.64 
L 624.237311 496.44 
L 624.320075 496.44 
L 624.320075 224.64 
L 624.237311 224.64 
z
" style="fill:#f4e1e1;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.320494 224.64 
L 624.320494 496.44 
L 624.369549 496.44 
L 624.369549 224.64 
L 624.320494 224.64 
z
" style="fill:#f3dbdb;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.369968 224.64 
L 624.369968 496.44 
L 624.414494 496.44 
L 624.414494 224.64 
L 624.369968 224.64 
z
" style="fill:#f4dfdf;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.414494 224.64 
L 624.414494 496.44 
L 624.470089 496.44 
L 624.470089 224.64 
L 624.414494 224.64 
z
" style="fill:#fefdfd;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 624.470089 224.64 
L 624.470089 496.44 
L 629.522117 496.44 
L 629.522117 224.64 
L 624.470089 224.64 
z
" style="fill:#d9d9f2;"/>
    <path clip-path="url(#p9901fb19d8)" d="M 629.522117 224.64 
L 629.522117 496.44 
L 629.542284 496.44 
L 629.542284 224.64 
L 629.522117 224.64 
z
" style="fill:#fdfdfe;"/>
   </g>
   <g id="line2d_30">
    <path clip-path="url(#p9901fb19d8)" d="M 152.401803 279 
L 152.401803 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_31">
    <path clip-path="url(#p9901fb19d8)" d="M 193.186437 279 
L 193.186437 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_32">
    <path clip-path="url(#p9901fb19d8)" d="M 226.383345 279 
L 226.383345 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_33">
    <path clip-path="url(#p9901fb19d8)" d="M 258.414936 279 
L 258.414936 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_34">
    <path clip-path="url(#p9901fb19d8)" d="M 288.754063 279 
L 288.754063 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_35">
    <path clip-path="url(#p9901fb19d8)" d="M 317.435021 279 
L 317.435021 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_36">
    <path clip-path="url(#p9901fb19d8)" d="M 344.122059 279 
L 344.122059 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_37">
    <path clip-path="url(#p9901fb19d8)" d="M 368.65833 279 
L 368.65833 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_38">
    <path clip-path="url(#p9901fb19d8)" d="M 392.330739 279 
L 392.330739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_39">
    <path clip-path="url(#p9901fb19d8)" d="M 415.053208 279 
L 415.053208 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_40">
    <path clip-path="url(#p9901fb19d8)" d="M 437.684739 279 
L 437.684739 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_41">
    <path clip-path="url(#p9901fb19d8)" d="M 460.129568 279 
L 460.129568 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_42">
    <path clip-path="url(#p9901fb19d8)" d="M 479.43428 279 
L 479.43428 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_43">
    <path clip-path="url(#p9901fb19d8)" d="M 497.427518 279 
L 497.427518 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_44">
    <path clip-path="url(#p9901fb19d8)" d="M 514.621041 279 
L 514.621041 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_45">
    <path clip-path="url(#p9901fb19d8)" d="M 529.764086 279 
L 529.764086 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_46">
    <path clip-path="url(#p9901fb19d8)" d="M 543.381133 279 
L 543.381133 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_47">
    <path clip-path="url(#p9901fb19d8)" d="M 556.465146 279 
L 556.465146 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_48">
    <path clip-path="url(#p9901fb19d8)" d="M 566.379734 279 
L 566.379734 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_49">
    <path clip-path="url(#p9901fb19d8)" d="M 576.939494 279 
L 576.939494 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_50">
    <path clip-path="url(#p9901fb19d8)" d="M 585.009465 279 
L 585.009465 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_51">
    <path clip-path="url(#p9901fb19d8)" d="M 593.603522 279 
L 593.603522 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="line2d_52">
    <path clip-path="url(#p9901fb19d8)" d="M 619.641867 279 
L 619.641867 7.2 
" style="fill:none;stroke:#000000;stroke-linecap:round;stroke-width:0.5;"/>
   </g>
   <g id="patch_3">
    <path d="M 110.602284 279 
L 110.602284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_4">
    <path d="M 629.542284 279 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
   <g id="patch_5">
    <path d="M 110.602284 279 
L 629.542284 279 
" style="fill:none;"/>
   </g>
   <g id="patch_6">
    <path d="M 110.602284 7.2 
L 629.542284 7.2 
" style="fill:none;"/>
   </g>
  </g>
  <g id="axes_2">
   <g id="patch_7">
    <path clip-path="url(#p26cbee16e5)" d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:#eaeaf2;stroke:#eaeaf2;stroke-linejoin:miter;stroke-width:0.01;"/>
   </g>
   <g id="matplotlib.axis_3"/>
   <g id="matplotlib.axis_4">
    <g id="ytick_6">
     <g id="line2d_53"/>
     <g id="text_32">
      <!-- −1 -->
      <defs>
       <path d="M 10.59375 35.5 
L 73.1875 35.5 
L 73.1875 27.203125 
L 10.59375 27.203125 
z
" id="DejaVuSans-2212"/>
      </defs>
      <g style="fill:#262626;" transform="translate(661.436284 208.207489)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-2212"/>
       <use x="83.789062" xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="ytick_7">
     <g id="line2d_54"/>
     <g id="text_33">
      <!-- 0 -->
      <g style="fill:#262626;" transform="translate(661.436284 146.899219)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-30"/>
      </g>
     </g>
    </g>
    <g id="ytick_8">
     <g id="line2d_55"/>
     <g id="text_34">
      <!-- 1 -->
      <g style="fill:#262626;" transform="translate(661.436284 85.590948)scale(0.1 -0.1)">
       <use xlink:href="#DejaVuSans-31"/>
      </g>
     </g>
    </g>
    <g id="text_35">
     <!-- log2 -->
     <g style="fill:#262626;" transform="translate(684.536753 154.984297)rotate(-90)scale(0.11 -0.11)">
      <use xlink:href="#DejaVuSans-6c"/>
      <use x="27.783203" xlink:href="#DejaVuSans-6f"/>
      <use x="88.964844" xlink:href="#DejaVuSans-67"/>
      <use x="152.441406" xlink:href="#DejaVuSans-32"/>
     </g>
    </g>
   </g>
   <image height="162.72" id="imagec7522deda6" transform="scale(1 -1)translate(0 -162.72)" width="7.92" x="646.56" xlink:href="data:image/png;base64,
iVBORw0KGgoAAAANSUhEUgAAAAsAAADiCAYAAACY5z1sAAAABHNCSVQICAgIfAhkiAAAAKlJREFUaIHt2DEOgDAMQ9E0yv3PxMGqlpWxyWA16DNHT2BZHhjuz7bDJ9xPT83CfWSO+8kRV7zG7+Vkzv0+kOi6y0yBRqbPZZnoNDJToJHpc1kmOo3MFGhk+qyR6XNZJjqNzBR8j4cd/9uz2Gsljuc8P7aUnDnuKBOdSM7k3PID75Dpc1kmOpHMFEhk+lyWiU4kMwUSmT6XZaITyUyBRKbPZZnoRHK/KXgBAOQmU71dszAAAAAASUVORK5CYII=" y="-61.2"/>
   <g id="patch_8">
    <path d="M 646.282284 224.64 
L 646.282284 224.002969 
L 646.282284 62.197031 
L 646.282284 61.56 
L 654.436284 61.56 
L 654.436284 62.197031 
L 654.436284 224.002969 
L 654.436284 224.64 
z
" style="fill:none;"/>
   </g>
  </g>
 </g>
 <defs>
  <clipPath id="p9901fb19d8">
   <rect height="271.8" width="518.94" x="110.602284" y="7.2"/>
  </clipPath>
  <clipPath id="p26cbee16e5">
   <rect height="163.08" width="8.154" x="646.282284" y="61.56"/>
  </clipPath>
 </defs>
</svg>
">
          

        

        

          

          

            

            

            
          

        

        

          

          

            
No Amplifications or Homozygous losses for Oncogenes
              or TSGs

          

        

        

          

          

            
SNV Results:

            

          

        

        

          

          

            
          

        

        

          

          

            
SNV Likely Drivers:

          

        

        

          

          

            
            

              
              
                  
                    
                    
                    
                    
                    
                    
                    
                    
                    
                    
                    
                    
                    
                  
                

                
                  

                    CHR
                    START
                    GENE
                    EFFECT
                    cDNA_CHANGE
                    PROTEIN_CHANGE
                    TARGET_VAF
                    REFERENCE_VAF
                    REFERENCE_DEPTH
                    Oncogene
                    TSG
                    CCF
                    GENE_TPM
                  

                
                
                  
                  
                  
                  
                  
                  
                  
                  
                  
                  
                  
                  
                  
                

                
                  

                    3
                    178917478
                    PIK3CA
                    non_synonymous_codon
                    
                    c.353G>A
                    p.G118D
                    0.35
                    0
                    37
                    ✔
                    
                    0.785316
                    9.70179
                  

                
                
              

            

          

        

        

          

          

            

            

            
          

        

        

          

          

            
Indel Results:

            

          

        

        

          

          

            

            
          

        

        

          

          

            
Indel Likely Drivers:

          

        

        

          

          

            
No Indel Likely Drivers

          

        

        

          

          

            

            
          

        

        

          

          

            
Rearrangement Results:
            

            

          

        

        

          

          

            
Rearranged Tumor Suppressor Genes:

          

        

        

          

          

            
            

              
              
                  
                    
                    
                    
                    
                  
                

                
                  

                    gene1
                    gene2
                    svclass
                    brass_score
                  

                
                
                  
                  
                  
                  
                

                
                  

                    EPHB2
                    BACH2
                    translocation
                    45
                  

                  

                    AGAP1
                    HDAC4
                    inversion
                    43
                  

                  

                    _
                    HDAC4
                    inversion
                    29
                  

                  

                    _
                    NF2
                    translocation
                    43
                  

                  

                    TERT
                    TERT
                    deletion
                    5
                  

                
                
              

            

          

        

        

          

          

            
Rearranged Oncogenes:

          

        

        

          

          

            
            

              
              
                  
                    
                    
                    
                    
                  
                

                
                  

                    gene1
                    gene2
                    svclass
                    brass_score
                  

                
                
                  
                  
                  
                  
                

                
                  

                    AGAP1
                    HDAC4
                    inversion
                    43
                  

                  

                    _
                    HDAC4
                    inversion
                    29
                  

                  

                    TERT
                    TERT
                    deletion
                    5
                  

                  

                    COL4A3BP
                    ROS1
                    translocation
                    37
                  

                  

                    KSR2
                    KSR2
                    tandem-duplication
                    
                    46
                  

                
                
              

            

          

        

        

          

          

            
Calls by Numbers:

            

          

        

        

          

          

            
            

              
              
                  
                    
                    
                    
                    
                    
                    
                    
                    
                  
                

                
                  

                    
                    SNVS
                    Coding SNVS
                    INDELS
                    Coding INDELS
                    #Coding/Mb
                    #Muts/Mb
                    REARR
                  

                
                
                  
                  
                  
                  
                  
                  
                  
                  
                

                
                  

                    
                      I-H-108333-T2-2-D1-1
                    3575
                    44
                    490
                    3
                    1.57
                    1.40
                    61
                  

                
                
              

            

          

        

        

          

          

            
Integrated Circos:

            

          

        

        

          

          

            
          

        

        

          

          

            
Mutational Signatures

            

          

        

        

          

          

            
          

        

        

          

          

            

            

            
          

        

        

          

          

            

            
END REPORT